Query 032363
Match_columns 142
No_of_seqs 125 out of 921
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 13:07:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032363.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032363hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0211 RpmA Ribosomal protein 100.0 1.2E-48 2.6E-53 283.2 8.9 86 55-140 1-86 (87)
2 KOG4600 Mitochondrial ribosoma 100.0 6.1E-48 1.3E-52 299.9 9.6 112 14-140 2-115 (144)
3 CHL00121 rpl27 ribosomal prote 100.0 7.6E-47 1.6E-51 273.6 9.4 85 55-139 1-85 (86)
4 PRK05435 rpmA 50S ribosomal pr 100.0 2.1E-46 4.6E-51 269.3 9.3 82 55-136 1-82 (82)
5 PF01016 Ribosomal_L27: Riboso 100.0 5.2E-46 1.1E-50 266.5 7.7 81 56-136 1-81 (81)
6 TIGR00062 L27 ribosomal protei 100.0 1.3E-45 2.7E-50 265.8 8.8 82 55-136 1-83 (83)
7 PF14382 ECR1_N: Exosome compl 95.6 0.026 5.7E-07 35.5 4.2 38 84-124 1-38 (39)
8 PRK09521 exosome complex RNA-b 95.4 0.05 1.1E-06 42.8 6.1 53 81-139 4-56 (189)
9 COG1096 Predicted RNA-binding 93.4 0.24 5.2E-06 40.9 6.0 55 80-140 3-57 (188)
10 PRK04163 exosome complex RNA-b 92.8 0.34 7.3E-06 39.7 6.0 52 79-139 5-56 (235)
11 PF03961 DUF342: Protein of un 88.2 1.4 3E-05 38.9 6.0 51 83-138 107-181 (451)
12 PF01551 Peptidase_M23: Peptid 86.4 1.7 3.8E-05 29.7 4.6 39 98-136 1-40 (96)
13 PRK14844 bifunctional DNA-dire 73.6 6.2 0.00014 43.4 5.5 63 77-139 2526-2601(2836)
14 PF13533 Biotin_lipoyl_2: Biot 66.7 5.4 0.00012 25.3 2.1 17 77-93 16-32 (50)
15 COG1315 Uncharacterized conser 66.6 6.8 0.00015 37.0 3.6 36 97-138 219-255 (543)
16 PRK09603 bifunctional DNA-dire 64.4 13 0.00028 41.3 5.5 63 77-139 2616-2692(2890)
17 TIGR02994 ectoine_eutE ectoine 63.2 11 0.00024 32.5 4.0 43 78-127 269-312 (325)
18 cd06850 biotinyl_domain The bi 62.9 26 0.00056 21.5 4.7 39 77-125 13-51 (67)
19 COG1097 RRP4 RNA-binding prote 57.9 23 0.0005 30.3 5.0 53 79-139 5-57 (239)
20 PF13375 RnfC_N: RnfC Barrel s 52.9 18 0.00038 26.5 3.1 33 79-122 46-78 (101)
21 PRK05889 putative acetyl-CoA c 51.6 25 0.00055 23.2 3.5 40 75-124 14-53 (71)
22 cd06253 M14_ASTE_ASPA_like_3 A 48.4 30 0.00065 29.2 4.2 42 79-127 244-285 (298)
23 cd06663 Biotinyl_lipoyl_domain 40.3 48 0.001 21.3 3.4 38 77-124 19-56 (73)
24 PRK09774 fec operon regulator 35.1 91 0.002 26.3 5.1 39 84-126 169-207 (319)
25 cd06251 M14_ASTE_ASPA_like_1 A 34.2 60 0.0013 27.0 3.8 40 79-126 234-273 (287)
26 PF13540 RCC1_2: Regulator of 32.9 52 0.0011 18.8 2.4 20 105-124 4-23 (30)
27 cd06254 M14_ASTE_ASPA_like_4 A 32.6 70 0.0015 26.6 4.0 42 78-127 237-278 (288)
28 PRK13918 CRP/FNR family transc 32.4 1.5E+02 0.0032 22.1 5.4 19 111-129 27-45 (202)
29 PRK06549 acetyl-CoA carboxylas 32.1 69 0.0015 24.6 3.6 44 70-123 68-111 (130)
30 PRK14875 acetoin dehydrogenase 31.8 61 0.0013 26.0 3.4 43 71-123 16-58 (371)
31 PRK11637 AmiB activator; Provi 30.4 65 0.0014 28.2 3.6 45 81-126 304-355 (428)
32 PRK08225 acetyl-CoA carboxylas 28.7 96 0.0021 20.1 3.4 37 77-123 15-51 (70)
33 TIGR00830 PTBA PTS system, glu 28.4 55 0.0012 24.9 2.5 16 109-124 34-49 (121)
34 PF00412 LIM: LIM domain; Int 27.8 48 0.001 20.3 1.8 21 82-102 5-25 (58)
35 PF00358 PTS_EIIA_1: phosphoen 27.1 52 0.0011 25.3 2.2 16 109-124 38-53 (132)
36 PRK09439 PTS system glucose-sp 26.4 65 0.0014 25.8 2.7 15 109-123 56-70 (169)
37 cd00210 PTS_IIA_glc PTS_IIA, P 26.2 62 0.0013 24.7 2.4 16 109-124 34-49 (124)
38 COG4687 Uncharacterized protei 26.2 86 0.0019 24.6 3.2 42 85-126 22-84 (122)
39 PF02471 OspE: Borrelia outer 25.6 56 0.0012 25.1 2.1 41 81-121 14-54 (108)
40 PF00529 HlyD: HlyD family sec 23.7 51 0.0011 26.0 1.6 17 77-93 15-31 (305)
41 COG5455 Predicted integral mem 23.1 82 0.0018 24.9 2.6 24 95-124 101-124 (129)
42 TIGR01015 hmgA homogentisate 1 22.9 69 0.0015 29.6 2.5 20 81-100 166-185 (429)
43 PF02749 QRPTase_N: Quinolinat 22.9 56 0.0012 22.7 1.5 20 77-96 49-68 (88)
44 PLN02658 homogentisate 1,2-dio 22.8 69 0.0015 29.7 2.5 21 80-100 164-184 (435)
45 TIGR02388 rpoC2_cyan DNA-direc 22.1 1.8E+02 0.0039 30.4 5.4 40 95-138 641-680 (1227)
46 COG1726 NqrA Na+-transporting 22.1 2E+02 0.0043 26.9 5.2 55 67-132 33-87 (447)
47 PF07177 Neuralized: Neuralize 21.5 73 0.0016 21.8 1.8 19 97-115 2-23 (69)
48 PF07370 DUF1489: Protein of u 21.3 65 0.0014 25.6 1.8 41 84-125 52-92 (137)
49 PRK01202 glycine cleavage syst 20.9 1.2E+02 0.0026 22.8 3.0 31 82-122 48-78 (127)
50 CHL00117 rpoC2 RNA polymerase 20.4 1.4E+02 0.0031 31.3 4.3 45 77-126 406-453 (1364)
No 1
>COG0211 RpmA Ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.2e-48 Score=283.15 Aligned_cols=86 Identities=65% Similarity=1.020 Sum_probs=84.4
Q ss_pred eeeccCCCcCCCCCCCCCccceeEeeCCeEeecCcEEeecccceEEcCCCeeecccceEEEeeceEEEEEEeCCCceEEE
Q 032363 55 SAHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVKFEKFGPDRKQVK 134 (142)
Q Consensus 55 ~A~KKggGSTkNGRdS~~KrLGvK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~F~k~~p~r~~V~ 134 (142)
|||||++|||+|||||++||||+|+++||.|.+|+||||||||+||||+|||+|+|||||||+||+|+|++..++|+||+
T Consensus 1 mA~KKg~GSt~NgRDS~~krLGvK~~~Gq~v~aG~IivRQRGTk~hpG~NVG~GkDhTlFAl~dG~Vkf~~k~~~rk~vs 80 (87)
T COG0211 1 MAHKKGGGSTRNGRDSESKRLGVKKFGGQFVKAGSIIVRQRGTKFHPGVNVGRGKDHTLFALVDGVVKFETKGKNRKYVS 80 (87)
T ss_pred CcccccccccccCccccccccceeeeCCeEEecccEEEEeccccccCCcccccCCCceEEEeeccEEEEEEccCCccEEE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999988999999
Q ss_pred EEecCC
Q 032363 135 YFAITN 140 (142)
Q Consensus 135 V~p~~~ 140 (142)
|+|+++
T Consensus 81 V~~~~~ 86 (87)
T COG0211 81 VVPEAE 86 (87)
T ss_pred EEeecc
Confidence 999875
No 2
>KOG4600 consensus Mitochondrial ribosomal protein MRP7 (L2) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.1e-48 Score=299.86 Aligned_cols=112 Identities=56% Similarity=0.787 Sum_probs=100.5
Q ss_pred eeeeeeccCCccceeecCceeccccceecCCCCCCcceeEEeeeccCCCcCCCCCCCCCccceeEeeCCeEeecCcEEee
Q 032363 14 FKGLSLSSSSSSSFLKGDFTVCPKSVTVSLPPTSPLPLTIESAHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVR 93 (142)
Q Consensus 14 f~glsl~s~~sss~~~g~~~~~~~~~~~~~~~~~~~~~~ir~A~KKggGSTkNGRdS~~KrLGvK~~~Gq~V~~G~IIvR 93 (142)
+++|.|++ +|+++.|+.+.+ ..+.||+|+||++|||||+|||+|+|||||+|+||+|+|||||+|
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 67788888 566777765443 356899999999999999999999999999999999999999999
Q ss_pred cccceEEcCCCeeecccceEEEeeceEEEEEEe--CCCceEEEEEecCC
Q 032363 94 QRGTKFHPGKNVGLGKDHTIFSLIDGLVKFEKF--GPDRKQVKYFAITN 140 (142)
Q Consensus 94 QRGtkfhPG~NVg~GrD~TLfAl~~G~V~F~k~--~p~r~~V~V~p~~~ 140 (142)
|||||||||+|||||||||||||++|+|+|++. .|.|++|+|.|.++
T Consensus 67 QRgtkfHPG~nVGiGKDhtifaL~eG~Vrf~k~~~~~~Rk~i~V~~~~~ 115 (144)
T KOG4600|consen 67 QRGTKFHPGDNVGIGKDHTIFALEEGRVRFEKSKITPPRKWIGVDPRGG 115 (144)
T ss_pred ecccccCCCcccccCCcceEEEeeccEEEEEEccCCCCcceEEEeecCC
Confidence 999999999999999999999999999999986 56789999999754
No 3
>CHL00121 rpl27 ribosomal protein L27; Reviewed
Probab=100.00 E-value=7.6e-47 Score=273.60 Aligned_cols=85 Identities=59% Similarity=0.949 Sum_probs=82.5
Q ss_pred eeeccCCCcCCCCCCCCCccceeEeeCCeEeecCcEEeecccceEEcCCCeeecccceEEEeeceEEEEEEeCCCceEEE
Q 032363 55 SAHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVKFEKFGPDRKQVK 134 (142)
Q Consensus 55 ~A~KKggGSTkNGRdS~~KrLGvK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~F~k~~p~r~~V~ 134 (142)
|||||++|||+|||||+|||||+|+++||+|.||+||||||||+||||+||||||||||||+++|+|+|++...++++|+
T Consensus 1 mA~KK~~GStkNgrdS~~KrLGvK~~~gq~V~~G~IivRQRGtk~hPG~NVg~GrD~TlfAl~~G~V~f~~~~~~~~~vs 80 (86)
T CHL00121 1 MAHKKGAGSTKNGRDSNAKRLGVKRFGGEKVSAGNILIRQRGTKFKPGLNVGCGKDFTLYALIDGFVKFKKKNKKQKSIN 80 (86)
T ss_pred CCcccccCcCCCCCCCCcccceeEEcCCEEEcCCcEEEEcCCCeECCCCcccccCCceEEEccceEEEEEEeCCCCEEEE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999998877899999
Q ss_pred EEecC
Q 032363 135 YFAIT 139 (142)
Q Consensus 135 V~p~~ 139 (142)
|+|..
T Consensus 81 v~~~~ 85 (86)
T CHL00121 81 VINIV 85 (86)
T ss_pred Eeecc
Confidence 99963
No 4
>PRK05435 rpmA 50S ribosomal protein L27; Validated
Probab=100.00 E-value=2.1e-46 Score=269.32 Aligned_cols=82 Identities=68% Similarity=1.076 Sum_probs=80.1
Q ss_pred eeeccCCCcCCCCCCCCCccceeEeeCCeEeecCcEEeecccceEEcCCCeeecccceEEEeeceEEEEEEeCCCceEEE
Q 032363 55 SAHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVKFEKFGPDRKQVK 134 (142)
Q Consensus 55 ~A~KKggGSTkNGRdS~~KrLGvK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~F~k~~p~r~~V~ 134 (142)
|||||++|||+|||||+|||||||+++||+|.||+||||||||+||||+||+|||||||||+++|+|+|++..+++++|+
T Consensus 1 mA~KK~~GStkNgrdS~~krLGvK~~~g~~V~~G~IivRQRGtk~~PG~nVg~GrD~TlfA~~~G~V~f~~~~~~~~~v~ 80 (82)
T PRK05435 1 MAHKKGGGSTRNGRDSESKRLGVKRFGGQFVKAGNIIVRQRGTKFHPGVNVGRGKDHTLFALVDGVVKFERKGRNRKYVS 80 (82)
T ss_pred CCcccccCcCCCCCCCCcccceeEecCCEEEcCCcEEEEeCCCeECCCCCEeecCCceEEEecceEEEEEEcCCCcEEEE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999998878899999
Q ss_pred EE
Q 032363 135 YF 136 (142)
Q Consensus 135 V~ 136 (142)
|+
T Consensus 81 v~ 82 (82)
T PRK05435 81 VV 82 (82)
T ss_pred EC
Confidence 85
No 5
>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=100.00 E-value=5.2e-46 Score=266.46 Aligned_cols=81 Identities=68% Similarity=1.056 Sum_probs=74.1
Q ss_pred eeccCCCcCCCCCCCCCccceeEeeCCeEeecCcEEeecccceEEcCCCeeecccceEEEeeceEEEEEEeCCCceEEEE
Q 032363 56 AHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVKFEKFGPDRKQVKY 135 (142)
Q Consensus 56 A~KKggGSTkNGRdS~~KrLGvK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~F~k~~p~r~~V~V 135 (142)
||||++|||+|||||+|||||||+++||+|.||+||||||||+||||+||+|||||||||++||+|+|++..+++++|+|
T Consensus 1 A~KK~~GSt~NgrdS~~krlGvK~~~G~~V~~G~IivRQRgtk~hPG~NVg~GrD~TLfAl~~G~V~f~~~~~~rk~v~V 80 (81)
T PF01016_consen 1 AHKKGGGSTKNGRDSNPKRLGVKKFGGQFVKAGNIIVRQRGTKFHPGENVGMGRDHTLFALVDGRVKFTKEKRNRKYVSV 80 (81)
T ss_dssp --SSSSSSSS--S-STTTTSEESSSTTCEESSTSEEEEBSSSSSEEBTTEEEETTSEEEESSSCEEEEEEETTTEEEEEE
T ss_pred CCccccccccCCCCCCCcccEEEEeCCEEEcCCCEEEEeCCCcCcCCCCEEECCCCcEEEecCEEEEEEEeCCCCEEEEe
Confidence 89999999999999999999999999999999999999999999999999999999999999999999998888999999
Q ss_pred E
Q 032363 136 F 136 (142)
Q Consensus 136 ~ 136 (142)
+
T Consensus 81 ~ 81 (81)
T PF01016_consen 81 V 81 (81)
T ss_dssp -
T ss_pred C
Confidence 6
No 6
>TIGR00062 L27 ribosomal protein L27. Eubacterial, chloroplast, and mitochondrial. Mitochondrial members have an additional C-terminal domain.
Probab=100.00 E-value=1.3e-45 Score=265.75 Aligned_cols=82 Identities=67% Similarity=1.019 Sum_probs=79.0
Q ss_pred eeeccCCCcCCCCCCCCCccceeEeeCCeEeecCcEEeecccceEEcCCCeeecccceEEEeeceEEEEEEeC-CCceEE
Q 032363 55 SAHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVKFEKFG-PDRKQV 133 (142)
Q Consensus 55 ~A~KKggGSTkNGRdS~~KrLGvK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~F~k~~-p~r~~V 133 (142)
|||||++|||+|||||+|||||||+++||+|.||+||||||||+||||+||+|||||||||+++|+|+|++.. +++++|
T Consensus 1 ~A~Kk~~GSt~NgrdS~~krLGvK~~~gq~V~~G~IivRQRGtk~hPG~nVg~GrD~TlfAl~~G~V~f~~~~~~~r~~v 80 (83)
T TIGR00062 1 MATKKGVGSTKNGRDSEAKRLGVKRAGGQFVRAGSIIVRQRGTKFHPGNNVGMGKDHTLFALSDGVVKFEKKGKRSRKFV 80 (83)
T ss_pred CCcccccCcCCCCCCCCCccceeEecCCEEEcCCcEEEEcCCceECCCCcccccCCCeEEEecceEEEEEEcCCCCCEEE
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999874 589999
Q ss_pred EEE
Q 032363 134 KYF 136 (142)
Q Consensus 134 ~V~ 136 (142)
+|+
T Consensus 81 ~v~ 83 (83)
T TIGR00062 81 SVV 83 (83)
T ss_pred EEC
Confidence 984
No 7
>PF14382 ECR1_N: Exosome complex exonuclease RRP4 N-terminal region; PDB: 2NN6_I 3M7N_C 2BA1_A 3M85_C.
Probab=95.63 E-value=0.026 Score=35.47 Aligned_cols=38 Identities=24% Similarity=0.557 Sum_probs=32.0
Q ss_pred EeecCcEEeecccceEEcCCCeeecccceEEEeeceEEEEE
Q 032363 84 VAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVKFE 124 (142)
Q Consensus 84 ~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~F~ 124 (142)
.|.||+.|... ..|.||.++.. +|..|||.+-|.|+..
T Consensus 1 iV~PG~~l~~~--~e~~~G~GTY~-~~g~I~asv~G~v~~~ 38 (39)
T PF14382_consen 1 IVVPGDRLGSS--EEYMPGHGTYV-RDGNIYASVAGTVKID 38 (39)
T ss_dssp EE-TT-EEEET--TTSEESTTEEE-ETTEEEESSSEEEEEE
T ss_pred CCCCCCEeecC--CCEecCCCEEE-eCCEEEEEeeEEEEEc
Confidence 48899999986 48899999999 9999999999999864
No 8
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=95.41 E-value=0.05 Score=42.77 Aligned_cols=53 Identities=11% Similarity=0.303 Sum_probs=43.6
Q ss_pred CCeEeecCcEEeecccceEEcCCCeeecccceEEEeeceEEEEEEeCCCceEEEEEecC
Q 032363 81 GDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVKFEKFGPDRKQVKYFAIT 139 (142)
Q Consensus 81 ~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~F~k~~p~r~~V~V~p~~ 139 (142)
+++.|.||+.|... -.|.||.|+.. +|..|||.+-|.++++. +++.|+|.|..
T Consensus 4 ~~~~V~PGe~l~~~--~e~~~G~Gty~-~~~~i~as~~G~~~id~---~~~~Isv~P~~ 56 (189)
T PRK09521 4 QGDLVLPGDYLAVI--EEYLPGEGTYE-DNGEVYASVVGKVFIDD---INRKISVIPFK 56 (189)
T ss_pred cCCEECCCCccccc--cceEcCCCEEe-eCCEEEEEeeEEEEEcC---CCCEEEEecCc
Confidence 67899999999765 36899999987 68889999999999853 45678888754
No 9
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=93.41 E-value=0.24 Score=40.88 Aligned_cols=55 Identities=15% Similarity=0.196 Sum_probs=46.5
Q ss_pred eCCeEeecCcEEeecccceEEcCCCeeecccceEEEeeceEEEEEEeCCCceEEEEEecCC
Q 032363 80 FGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVKFEKFGPDRKQVKYFAITN 140 (142)
Q Consensus 80 ~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~F~k~~p~r~~V~V~p~~~ 140 (142)
-.|.+|.||+.|..+ -.|.||+++--= |+.|+|...|.+..+.. .+.++|.|...
T Consensus 3 ~~g~~v~PGd~~a~~--EE~~~G~gt~~~-~g~i~Aa~~G~~~~d~~---n~~~~V~p~~~ 57 (188)
T COG1096 3 KDGTFVLPGDVLAVI--EEFLPGEGTYEE-GGEIRAAATGVVRRDDK---NRVISVKPGKK 57 (188)
T ss_pred ccCcEEcCcceeeee--eeeecCCCeEeE-CCEEEEeecccEEEccc---ceEEEeccCCC
Confidence 468899999999976 489999999876 99999999999999764 47788888754
No 10
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=92.77 E-value=0.34 Score=39.73 Aligned_cols=52 Identities=19% Similarity=0.476 Sum_probs=42.0
Q ss_pred eeCCeEeecCcEEeecccceEEcCCCeeecccceEEEeeceEEEEEEeCCCceEEEEEecC
Q 032363 79 IFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVKFEKFGPDRKQVKYFAIT 139 (142)
Q Consensus 79 ~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~F~k~~p~r~~V~V~p~~ 139 (142)
+..+..|.||+.|.- -.|.||.|+.. +|..|+|.+-|.+.... +.++|.|..
T Consensus 5 ~~~~~~V~PGd~l~~---~~~~~G~Gty~-~~g~i~As~~G~~~~~~-----~~i~V~p~~ 56 (235)
T PRK04163 5 VEDRKIVVPGDLLAE---GEFKAGRGTYK-ENGKIYSTVVGLVDIKD-----DKVRVIPLE 56 (235)
T ss_pred eeCCcEECCCCCcCc---CCeecCCceEE-eCCEEEEEEeEEEEEEC-----CEEEEEECC
Confidence 456789999999963 36999999987 89999999999999753 267777753
No 11
>PF03961 DUF342: Protein of unknown function (DUF342); InterPro: IPR005646 This family of bacterial proteins has no known function. The proteins are in the region of 500-600 amino acid residues in length.
Probab=88.21 E-value=1.4 Score=38.86 Aligned_cols=51 Identities=24% Similarity=0.458 Sum_probs=39.4
Q ss_pred eEeecCcEEeecc----c------------------ceEEcCCCeeec-cc-ceEEEeeceEEEEEEeCCCceEEEEEec
Q 032363 83 QVAKPGAIIVRQR----G------------------TKFHPGKNVGLG-KD-HTIFSLIDGLVKFEKFGPDRKQVKYFAI 138 (142)
Q Consensus 83 q~V~~G~IIvRQR----G------------------tkfhPG~NVg~G-rD-~TLfAl~~G~V~F~k~~p~r~~V~V~p~ 138 (142)
+.|.+|+.|++-- | ..|.+|+|+-+- .| .+|+|.++|++.|+.. .++|.|.
T Consensus 107 ~~V~~G~~la~~~p~~~G~~G~~V~G~~I~~~~~~~~~~~~g~~~~~~~~d~~~~~A~~~G~~~~~~~-----~i~V~~~ 181 (451)
T PF03961_consen 107 PSVKKGDVLAEKIPPTPGEPGRDVFGEPIPAKPGKDIPLKAGKNTEVSEEDGNKLYAAIDGRPVFENG-----KISVDPV 181 (451)
T ss_pred eEECCCCEEEEEccCCCCCCCcccCCCCcCCCCCCccceeCCCCEEEEcCCCCEEEEecCCEEEEECC-----EEEEEEe
Confidence 3488888888743 2 678899999999 76 4799999999999842 2666664
No 12
>PF01551 Peptidase_M23: Peptidase family M23; InterPro: IPR016047 Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins such as Swiss:P33648 for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown.; PDB: 3IT5_A 3IT7_B 2GU1_A 3NYY_A 2HSI_B 3SLU_B 3UZ0_D 3TUF_B 1QWY_A 2B44_B ....
Probab=86.45 E-value=1.7 Score=29.69 Aligned_cols=39 Identities=23% Similarity=0.331 Sum_probs=27.3
Q ss_pred eEEcCCCeeecccceEEEeeceEEEEEEeCC-CceEEEEE
Q 032363 98 KFHPGKNVGLGKDHTIFSLIDGLVKFEKFGP-DRKQVKYF 136 (142)
Q Consensus 98 kfhPG~NVg~GrD~TLfAl~~G~V~F~k~~p-~r~~V~V~ 136 (142)
|||.|-.+.......++|+.+|+|.|....+ .-.+|.|.
T Consensus 1 r~h~Gid~~~~~g~~V~A~~~G~V~~~~~~~~~g~~V~i~ 40 (96)
T PF01551_consen 1 RFHNGIDFAAPEGTPVYAPADGKVVFVGEDPGYGNYVIIQ 40 (96)
T ss_dssp -EE-SEEEEETTT-EEEESSSEEEEEEEEETTTEEEEEEE
T ss_pred CCeeeEEeCCCCCCEEEeCccEEEEEEEeccCCccEEEEE
Confidence 6889988888888889999999999966532 24455544
No 13
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=73.63 E-value=6.2 Score=43.45 Aligned_cols=63 Identities=27% Similarity=0.407 Sum_probs=41.9
Q ss_pred eEeeCCeEeecCcEEee-cccc----eEEcCC-------CeeecccceEEEeeceEEEE-EEeCCCceEEEEEecC
Q 032363 77 VKIFGDQVAKPGAIIVR-QRGT----KFHPGK-------NVGLGKDHTIFSLIDGLVKF-EKFGPDRKQVKYFAIT 139 (142)
Q Consensus 77 vK~~~Gq~V~~G~IIvR-QRGt----kfhPG~-------NVg~GrD~TLfAl~~G~V~F-~k~~p~r~~V~V~p~~ 139 (142)
+-+.+||.|.+|+||+| -|-+ -+--|. -...-||+.+.|.+||+|.| ++..+.++.|.|.|.+
T Consensus 2526 l~v~~g~~v~~Gdilakipr~~~~t~DIT~GLpRv~eLFEar~pk~~a~isei~G~V~~~~~~~~~~~~i~i~~~~ 2601 (2836)
T PRK14844 2526 LNVQDGQKVHAGDVITRTPRESVKTRDITGGLPRVIELFEARRPKEHAIVSEIDGYVAFSEKDRRGKRSILIKPVD 2601 (2836)
T ss_pred EeeccCceecccceeecccccccccCccCCCCccchheeeeecCCCceEEecCCcEEEecccccCCceEEEEECCC
Confidence 45679999999999998 2211 011221 12356789999999999999 3322446677777753
No 14
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=66.71 E-value=5.4 Score=25.29 Aligned_cols=17 Identities=24% Similarity=0.321 Sum_probs=14.9
Q ss_pred eEeeCCeEeecCcEEee
Q 032363 77 VKIFGDQVAKPGAIIVR 93 (142)
Q Consensus 77 vK~~~Gq~V~~G~IIvR 93 (142)
+.+-.||+|++|++|++
T Consensus 16 v~V~~G~~VkkGd~L~~ 32 (50)
T PF13533_consen 16 VYVKEGQQVKKGDVLLV 32 (50)
T ss_pred EEecCCCEEcCCCEEEE
Confidence 55669999999999987
No 15
>COG1315 Uncharacterized conserved protein [Function unknown]
Probab=66.64 E-value=6.8 Score=37.04 Aligned_cols=36 Identities=31% Similarity=0.419 Sum_probs=29.9
Q ss_pred ceEEcCCCeeeccc-ceEEEeeceEEEEEEeCCCceEEEEEec
Q 032363 97 TKFHPGKNVGLGKD-HTIFSLIDGLVKFEKFGPDRKQVKYFAI 138 (142)
Q Consensus 97 tkfhPG~NVg~GrD-~TLfAl~~G~V~F~k~~p~r~~V~V~p~ 138 (142)
..+++|+|+- =|| .||.|.++|..-..+ ..|+|+|.
T Consensus 219 ~~l~lG~nt~-~kd~~tlvA~~~G~~~~s~-----~tI~V~~i 255 (543)
T COG1315 219 IKLNLGKNTA-FKDNNTLVAKRDGQPIVSK-----NTISVYPI 255 (543)
T ss_pred eeeecCCCCc-cCCCCEEEEeeCCeEEecC-----CeeEEEEE
Confidence 6899999999 555 899999999998754 56888885
No 16
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=64.40 E-value=13 Score=41.30 Aligned_cols=63 Identities=19% Similarity=0.288 Sum_probs=42.9
Q ss_pred eEeeCCeEeecCcEEee-cccce----EEcCC-------Cee--ecccceEEEeeceEEEEEEeCCCceEEEEEecC
Q 032363 77 VKIFGDQVAKPGAIIVR-QRGTK----FHPGK-------NVG--LGKDHTIFSLIDGLVKFEKFGPDRKQVKYFAIT 139 (142)
Q Consensus 77 vK~~~Gq~V~~G~IIvR-QRGtk----fhPG~-------NVg--~GrD~TLfAl~~G~V~F~k~~p~r~~V~V~p~~ 139 (142)
+-+.+|+.|.+|+||+| +|-+- +--|. -.. .=+|..+.|.+||+|+|.+..+.++.|.|.+.+
T Consensus 2616 l~v~~g~~v~~gdilak~p~~~~~t~DITgGLprv~eLfear~~~pk~~a~i~ei~G~v~~~~~~~~~~~i~i~~~~ 2692 (2890)
T PRK09603 2616 IAISDGSSVEQAEVLAKIPKATVKSRDITGGLPRVSELFEARKPKPKDVAILSEVDGIVSFGKPIRNKEHIIVTSKD 2692 (2890)
T ss_pred EEecCCCEecccceEeeccccccccccccCCcccchhheEeecCCCCCceEEeccceEEEeccccCCceEEEEECCC
Confidence 45678999999999998 44321 11111 011 356899999999999996543456778787764
No 17
>TIGR02994 ectoine_eutE ectoine utilization protein EutE. Members of this family, part of the succinylglutamate desuccinylase / aspartoacylase family (pfam04952), belong to ectoine utilization operons, as found in Sinorhizobium meliloti 1021 (where it the operon is known to be induced by ectoine), Mesorhizobium loti, Silicibacter pomeroyi, Agrobacterium tumefaciens, and Pseudomonas putida.
Probab=63.25 E-value=11 Score=32.52 Aligned_cols=43 Identities=21% Similarity=0.148 Sum_probs=32.1
Q ss_pred EeeCCeEeecCcEEeecccceEE-cCCCeeecccceEEEeeceEEEEEEeC
Q 032363 78 KIFGDQVAKPGAIIVRQRGTKFH-PGKNVGLGKDHTIFSLIDGLVKFEKFG 127 (142)
Q Consensus 78 K~~~Gq~V~~G~IIvRQRGtkfh-PG~NVg~GrD~TLfAl~~G~V~F~k~~ 127 (142)
++--|+.|++|++|.+..- +. +|+-+ ++|.|+.+|+|.+....
T Consensus 269 ~v~~G~~V~~G~~lg~I~d--~~~~G~~~-----~~i~Ap~dGiV~~~~~~ 312 (325)
T TIGR02994 269 MIDLGDPVSKGDVIARVYP--VGRTGVAP-----VEYRAKRDGLLAARHFP 312 (325)
T ss_pred ecCCCCEeCCCCEEEEEEC--CCCCCCce-----EEEEeCCCcEEEEEeCC
Confidence 3455899999999988765 32 45433 69999999999996643
No 18
>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=62.91 E-value=26 Score=21.47 Aligned_cols=39 Identities=13% Similarity=0.128 Sum_probs=29.7
Q ss_pred eEeeCCeEeecCcEEeecccceEEcCCCeeecccceEEEeeceEEEEEE
Q 032363 77 VKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVKFEK 125 (142)
Q Consensus 77 vK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~F~k 125 (142)
+.+-.|++|.+|+.|++=... ..+..|.|+.+|+|..-.
T Consensus 13 ~~v~~G~~v~~g~~l~~i~~~----------~~~~~i~ap~~G~v~~~~ 51 (67)
T cd06850 13 VLVKEGDKVEAGQPLAVLEAM----------KMENEVTAPVAGVVKEIL 51 (67)
T ss_pred EEeCCCCEECCCCEEEEEEcc----------cEEEEEeCCCCEEEEEEE
Confidence 666789999999999974321 125789999999997644
No 19
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=57.90 E-value=23 Score=30.33 Aligned_cols=53 Identities=17% Similarity=0.397 Sum_probs=37.8
Q ss_pred eeCCeEeecCcEEeecccceEEcCCCeeecccceEEEeeceEEEEEEeCCCceEEEEEecC
Q 032363 79 IFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVKFEKFGPDRKQVKYFAIT 139 (142)
Q Consensus 79 ~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~F~k~~p~r~~V~V~p~~ 139 (142)
....+.|.||+++.-+- .|..|.++.+ +|.-+||.+-|.|...- +.+.|+|.+
T Consensus 5 ~~~~~iV~PGd~vl~~~--~~~~G~Gty~-~~~~iyssv~G~~~~~~-----~~v~VIpl~ 57 (239)
T COG1097 5 VSMRKIVLPGDLVLAEG--SYKLGHGTYF-EGGKIYSSVVGLLDVKG-----KLVRVIPLE 57 (239)
T ss_pred ccccceecCCCccCCCC--CEecCCCcEe-cCCEEEEEEEeEEEEeC-----CEEEEEeCC
Confidence 45678899999754433 3455555555 99999999999999863 337777754
No 20
>PF13375 RnfC_N: RnfC Barrel sandwich hybrid domain
Probab=52.85 E-value=18 Score=26.54 Aligned_cols=33 Identities=21% Similarity=0.342 Sum_probs=25.1
Q ss_pred eeCCeEeecCcEEeecccceEEcCCCeeecccceEEEeeceEEE
Q 032363 79 IFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVK 122 (142)
Q Consensus 79 ~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~ 122 (142)
+--||+|+.|++|.+-.|. + .-.|+|.++|+|.
T Consensus 46 V~~Gd~V~~GQ~Ia~~~~~-------~----sa~iHAsvSG~V~ 78 (101)
T PF13375_consen 46 VKVGDKVKKGQLIAEAEGF-------L----SAPIHASVSGTVT 78 (101)
T ss_pred EcCCCEEcCCCEEEecCCC-------c----EeeEEcCCCeEEE
Confidence 4469999999999986541 1 1268999999985
No 21
>PRK05889 putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Provisional
Probab=51.59 E-value=25 Score=23.20 Aligned_cols=40 Identities=18% Similarity=0.182 Sum_probs=29.9
Q ss_pred ceeEeeCCeEeecCcEEeecccceEEcCCCeeecccceEEEeeceEEEEE
Q 032363 75 LGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVKFE 124 (142)
Q Consensus 75 LGvK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~F~ 124 (142)
.=|.+-.|+.|.+|+.|+-=--.| -++.|.|.++|+|.--
T Consensus 14 ~~~~v~~Gd~V~~g~~l~~ve~~K----------~~~~I~a~~~G~V~~i 53 (71)
T PRK05889 14 LEVVVNEGDQIGKGDTLVLLESMK----------MEIPVLAEVAGTVSKV 53 (71)
T ss_pred EEEEeCCCCEECCCCEEEEEEecc----------ceeEEeCCCCEEEEEE
Confidence 346778899999999998432222 3778999999998653
No 22
>cd06253 M14_ASTE_ASPA_like_3 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD.
Probab=48.44 E-value=30 Score=29.20 Aligned_cols=42 Identities=14% Similarity=0.086 Sum_probs=30.1
Q ss_pred eeCCeEeecCcEEeecccceEEcCCCeeecccceEEEeeceEEEEEEeC
Q 032363 79 IFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVKFEKFG 127 (142)
Q Consensus 79 ~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~F~k~~ 127 (142)
+--|+.|++|++|.+..-. ++|+- -+++.|+.||+|-+....
T Consensus 244 ~~~G~~V~~Gq~lg~i~dp--~~g~~-----~~~v~Ap~dGiv~~~~~~ 285 (298)
T cd06253 244 KHLGDIVKRGDVIGEIVDP--LEGEV-----IEEVIAPCDGILFTLREY 285 (298)
T ss_pred cCCCCEECCCCEEEEEeCC--CCCCe-----eEEEEcCCCeEEEEeecC
Confidence 4457889999998887652 23332 258999999999997643
No 23
>cd06663 Biotinyl_lipoyl_domains Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl, or methylamine, respectively, between components of the complex/protein via a biotinyl or lipoyl group, which is covalently attached to a highly conserved lysine residue.
Probab=40.26 E-value=48 Score=21.35 Aligned_cols=38 Identities=16% Similarity=0.050 Sum_probs=27.7
Q ss_pred eEeeCCeEeecCcEEeecccceEEcCCCeeecccceEEEeeceEEEEE
Q 032363 77 VKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVKFE 124 (142)
Q Consensus 77 vK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~F~ 124 (142)
+.+-.|+.|.+|+.|..=...| -...|.|+.+|+|.--
T Consensus 19 ~~v~~G~~v~~g~~l~~ie~~k----------~~~~i~ap~~G~v~~~ 56 (73)
T cd06663 19 WLKKVGDKVKKGDVLAEIEAMK----------ATSDVEAPKSGTVKKV 56 (73)
T ss_pred EEcCCcCEECCCCEEEEEEeCC----------eEEEEEcCCCEEEEEE
Confidence 6666888999998888732222 2567999999998653
No 24
>PRK09774 fec operon regulator FecR; Reviewed
Probab=35.10 E-value=91 Score=26.34 Aligned_cols=39 Identities=15% Similarity=0.065 Sum_probs=32.5
Q ss_pred EeecCcEEeecccceEEcCCCeeecccceEEEeeceEEEEEEe
Q 032363 84 VAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVKFEKF 126 (142)
Q Consensus 84 ~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~F~k~ 126 (142)
.|..|+.-|+--||+| ||-.-.+.+-.++.+|.|++...
T Consensus 169 ~V~t~~~~v~vlGT~F----~V~~~~~~~~V~V~eG~V~v~~~ 207 (319)
T PRK09774 169 RVLTRQGQLTALGTEF----TVRQQDNFTQLAVQQHAVEVLLA 207 (319)
T ss_pred EEEeCCcEEEEeeeEE----EEEEcCCCceEEEEEEEEEEEEC
Confidence 4777888899999999 57777788889999999999653
No 25
>cd06251 M14_ASTE_ASPA_like_1 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD.
Probab=34.20 E-value=60 Score=27.03 Aligned_cols=40 Identities=15% Similarity=0.171 Sum_probs=27.5
Q ss_pred eeCCeEeecCcEEeecccceEEcCCCeeecccceEEEeeceEEEEEEe
Q 032363 79 IFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVKFEKF 126 (142)
Q Consensus 79 ~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~F~k~ 126 (142)
+--|+.|.+|+.|.+..-. -| ....++.|+.+|.|.+...
T Consensus 234 ~~~Gd~V~~G~~ig~i~d~---~~-----~~~~~v~ap~~G~v~~~~~ 273 (287)
T cd06251 234 VKLGDKVKKGQLLATITDP---FG-----EEEAEVKAPFDGIVIGRNN 273 (287)
T ss_pred cCCCCEECCCCEEEEEECC---CC-----CceEEEECCCCeEEEEecC
Confidence 4457788888888776441 11 1127899999999987654
No 26
>PF13540 RCC1_2: Regulator of chromosome condensation (RCC1) repeat; PDB: 3QI0_D 1JTD_B 3QHY_B.
Probab=32.95 E-value=52 Score=18.79 Aligned_cols=20 Identities=30% Similarity=0.159 Sum_probs=16.2
Q ss_pred eeecccceEEEeeceEEEEE
Q 032363 105 VGLGKDHTIFSLIDGLVKFE 124 (142)
Q Consensus 105 Vg~GrD~TLfAl~~G~V~F~ 124 (142)
|-.|.+||+.=+.+|.|.--
T Consensus 4 ia~G~~ht~al~~~g~v~~w 23 (30)
T PF13540_consen 4 IACGGYHTCALTSDGEVYCW 23 (30)
T ss_dssp EEEESSEEEEEE-TTEEEEE
T ss_pred EEecCCEEEEEEcCCCEEEE
Confidence 67899999999999998653
No 27
>cd06254 M14_ASTE_ASPA_like_4 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD.
Probab=32.59 E-value=70 Score=26.56 Aligned_cols=42 Identities=14% Similarity=0.127 Sum_probs=30.3
Q ss_pred EeeCCeEeecCcEEeecccceEEcCCCeeecccceEEEeeceEEEEEEeC
Q 032363 78 KIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVKFEKFG 127 (142)
Q Consensus 78 K~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~F~k~~ 127 (142)
++--|+.|++|++|....-.- |+ ..+++.|+.||.|-+....
T Consensus 237 ~~~~G~~V~~G~~lg~i~dp~---g~-----~~~~i~Ap~dG~v~~~~~~ 278 (288)
T cd06254 237 FVKAGDTVQKGALLGYVTDYF---GN-----VIAEYRAPFDGVVLYNTAT 278 (288)
T ss_pred ecCCCCEecCCCEEEEEECCC---CC-----ceEEEEcCCCcEEEEeeCC
Confidence 445688889999988775422 32 2468999999999987643
No 28
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=32.36 E-value=1.5e+02 Score=22.10 Aligned_cols=19 Identities=16% Similarity=0.506 Sum_probs=15.9
Q ss_pred ceEEEeeceEEEEEEeCCC
Q 032363 111 HTIFSLIDGLVKFEKFGPD 129 (142)
Q Consensus 111 ~TLfAl~~G~V~F~k~~p~ 129 (142)
+.+|-+.+|.|+..+..++
T Consensus 27 ~~~y~I~~G~vr~~~~~~~ 45 (202)
T PRK13918 27 DMLYRVRSGLVRLHTVDDE 45 (202)
T ss_pred CeEEEEEeeEEEEEEECCC
Confidence 6799999999999886554
No 29
>PRK06549 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=32.07 E-value=69 Score=24.65 Aligned_cols=44 Identities=16% Similarity=0.111 Sum_probs=34.7
Q ss_pred CCCccceeEeeCCeEeecCcEEeecccceEEcCCCeeecccceEEEeeceEEEE
Q 032363 70 SRGQRLGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVKF 123 (142)
Q Consensus 70 S~~KrLGvK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~F 123 (142)
-.++=+=|..-.|+.|.+|+.|+.=.-.| -...|.|..+|+|..
T Consensus 68 ~~G~V~~i~V~~Gd~V~~Gq~L~~lEamK----------me~eI~Ap~~G~V~~ 111 (130)
T PRK06549 68 MPGTILKVLVAVGDQVTENQPLLILEAMK----------MENEIVASSAGTVTA 111 (130)
T ss_pred CCEEEEEEEeCCCCEECCCCEEEEEeccC----------ccEEEEcCCCeEEEE
Confidence 34566678999999999999999755444 257899999999965
No 30
>PRK14875 acetoin dehydrogenase E2 subunit dihydrolipoyllysine-residue acetyltransferase; Provisional
Probab=31.77 E-value=61 Score=26.04 Aligned_cols=43 Identities=9% Similarity=0.078 Sum_probs=31.4
Q ss_pred CCccceeEeeCCeEeecCcEEeecccceEEcCCCeeecccceEEEeeceEEEE
Q 032363 71 RGQRLGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVKF 123 (142)
Q Consensus 71 ~~KrLGvK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~F 123 (142)
.++=.-|.+-.|+.|.+|++|+.--. +--++.+-|+.+|+|.-
T Consensus 16 ~g~~~~~~~~~g~~v~~~~~~~~~e~----------~k~~~~~~a~~~g~~~~ 58 (371)
T PRK14875 16 EGKVAGWLVQEGDEVEKGDELLDVET----------DKITNEVEAPAAGTLRR 58 (371)
T ss_pred eEEEEEEEcCCCCEeCCCCEEEEEEe----------cceeEEEecCCCeEEEE
Confidence 34555678889999999999998222 22347788999998863
No 31
>PRK11637 AmiB activator; Provisional
Probab=30.38 E-value=65 Score=28.20 Aligned_cols=45 Identities=20% Similarity=0.390 Sum_probs=27.7
Q ss_pred CCeEeec--CcEEeecccceE-----EcCCCeeecccceEEEeeceEEEEEEe
Q 032363 81 GDQVAKP--GAIIVRQRGTKF-----HPGKNVGLGKDHTIFSLIDGLVKFEKF 126 (142)
Q Consensus 81 ~Gq~V~~--G~IIvRQRGtkf-----hPG~NVg~GrD~TLfAl~~G~V~F~k~ 126 (142)
.|.+.+| |.|+ .+=|.+. |.|-.+.-..+-.++|..+|+|.|..+
T Consensus 304 ~g~~~~Pv~g~i~-~~fg~~~~~~~~~~Gi~i~~~~g~~v~A~~~G~V~~~~~ 355 (428)
T PRK11637 304 RGQAFWPVRGPTL-HRFGEQLQGELRWKGMVIGASEGTEVKAIADGRVLLADW 355 (428)
T ss_pred CCCCccCCCCCcc-CCCCCCCCCCCCCCCEEeecCCCCeEEecCCeEEEEeec
Confidence 3555554 5443 3344444 444444545677899999999999643
No 32
>PRK08225 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=28.66 E-value=96 Score=20.12 Aligned_cols=37 Identities=19% Similarity=0.141 Sum_probs=27.8
Q ss_pred eEeeCCeEeecCcEEeecccceEEcCCCeeecccceEEEeeceEEEE
Q 032363 77 VKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVKF 123 (142)
Q Consensus 77 vK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~F 123 (142)
+.+-.|+.|.+|+.|..=.-.| ....+.|.++|+|.-
T Consensus 15 ~~v~~G~~V~~g~~l~~ve~~k----------~~~~v~s~~~G~v~~ 51 (70)
T PRK08225 15 IVVKVGDTVEEGQDVVILESMK----------MEIPIVAEEAGTVKK 51 (70)
T ss_pred EEeCCCCEECCCCEEEEEEcCC----------CcceEeCCCCEEEEE
Confidence 6677799999999998733322 267899999999854
No 33
>TIGR00830 PTBA PTS system, glucose subfamily, IIA component. These are part of the The PTS Glucose-Glucoside (Glc) SuperFamily. The Glc family includes permeases specific for glucose, N-acetylglucosamine and a large variety of a- and b-glucosides. However, not all b-glucoside PTS permeases are in this class, as the cellobiose (Cel) b-glucoside PTS permease is in the Lac family (TC #4.A.3). The IIA, IIB and IIC domains of all of the permeases listed below are demonstrably homologous. These permeases show limited sequence similarity with members of the Fru family (TC #4.A.2). Several of the PTS permeases in the Glc family lack their own IIA domains and instead use the glucose IIA protein (IIAglc or Crr). Most of these permeases have the B and C domains linked together in a single polypeptide chain, and a cysteyl residue in the IIB domain is phosphorylated by direct phosphoryl transfer from IIAglc(his~P). Those permeases which lack a IIA domain include the maltose (Mal), arbutin-salicin-c
Probab=28.42 E-value=55 Score=24.88 Aligned_cols=16 Identities=19% Similarity=0.289 Sum_probs=13.5
Q ss_pred ccceEEEeeceEEEEE
Q 032363 109 KDHTIFSLIDGLVKFE 124 (142)
Q Consensus 109 rD~TLfAl~~G~V~F~ 124 (142)
.|.++||+++|+|..-
T Consensus 34 ~~~~v~AP~~G~v~~v 49 (121)
T TIGR00830 34 TDGKVVAPVDGKIGKI 49 (121)
T ss_pred CCCeEEccCCeEEEEE
Confidence 4679999999999773
No 34
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=27.84 E-value=48 Score=20.29 Aligned_cols=21 Identities=19% Similarity=0.398 Sum_probs=17.4
Q ss_pred CeEeecCcEEeecccceEEcC
Q 032363 82 DQVAKPGAIIVRQRGTKFHPG 102 (142)
Q Consensus 82 Gq~V~~G~IIvRQRGtkfhPG 102 (142)
++.|.++.++++..|..|||-
T Consensus 5 ~~~I~~~~~~~~~~~~~~H~~ 25 (58)
T PF00412_consen 5 GKPIYGTEIVIKAMGKFWHPE 25 (58)
T ss_dssp SSBESSSSEEEEETTEEEETT
T ss_pred CCCccCcEEEEEeCCcEEEcc
Confidence 456778888889999999985
No 35
>PF00358 PTS_EIIA_1: phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1; InterPro: IPR001127 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. ; GO: 0005351 sugar:hydrogen symporter activity, 0006810 transport, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016020 membrane; PDB: 3OUR_D 1GPR_A 1F3G_A 2F3G_B 1F3Z_A 1O2F_A 1GLB_F 1GGR_A 1GLA_F 1GLE_F ....
Probab=27.11 E-value=52 Score=25.29 Aligned_cols=16 Identities=25% Similarity=0.542 Sum_probs=13.7
Q ss_pred ccceEEEeeceEEEEE
Q 032363 109 KDHTIFSLIDGLVKFE 124 (142)
Q Consensus 109 rD~TLfAl~~G~V~F~ 124 (142)
.|.+|||+++|.|..-
T Consensus 38 ~~~~v~AP~~G~v~~i 53 (132)
T PF00358_consen 38 SDGKVYAPVDGTVTMI 53 (132)
T ss_dssp SSSEEEESSSEEEEEE
T ss_pred CCCeEEEEeeEEEEEE
Confidence 5679999999999874
No 36
>PRK09439 PTS system glucose-specific transporter subunit; Provisional
Probab=26.35 E-value=65 Score=25.83 Aligned_cols=15 Identities=13% Similarity=0.328 Sum_probs=13.2
Q ss_pred ccceEEEeeceEEEE
Q 032363 109 KDHTIFSLIDGLVKF 123 (142)
Q Consensus 109 rD~TLfAl~~G~V~F 123 (142)
.|.++||+++|+|..
T Consensus 56 ~~~~v~AP~dG~V~~ 70 (169)
T PRK09439 56 TGNKMVAPVDGTIGK 70 (169)
T ss_pred cCCEEEecCCeEEEE
Confidence 568999999999976
No 37
>cd00210 PTS_IIA_glc PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation.
Probab=26.18 E-value=62 Score=24.66 Aligned_cols=16 Identities=19% Similarity=0.308 Sum_probs=13.4
Q ss_pred ccceEEEeeceEEEEE
Q 032363 109 KDHTIFSLIDGLVKFE 124 (142)
Q Consensus 109 rD~TLfAl~~G~V~F~ 124 (142)
.++++||+++|+|..-
T Consensus 34 ~~~~v~AP~~G~v~~i 49 (124)
T cd00210 34 SDGKVVAPVDGTIVQI 49 (124)
T ss_pred cCCeEECcCCeEEEEE
Confidence 3679999999999764
No 38
>COG4687 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.17 E-value=86 Score=24.63 Aligned_cols=42 Identities=31% Similarity=0.572 Sum_probs=36.4
Q ss_pred eecCcEEeecccceEEcCCCee---------------------ecccceEEEeeceEEEEEEe
Q 032363 85 AKPGAIIVRQRGTKFHPGKNVG---------------------LGKDHTIFSLIDGLVKFEKF 126 (142)
Q Consensus 85 V~~G~IIvRQRGtkfhPG~NVg---------------------~GrD~TLfAl~~G~V~F~k~ 126 (142)
+.-|.||+=..|..|++-.||. +||.+.|+-...|.|+|.-.
T Consensus 22 ~~~GkiliGDkgfEFYn~~nv~k~iqipWs~i~~v~vsvs~KK~~~~f~i~td~~gk~~FaSk 84 (122)
T COG4687 22 AEYGKILIGDKGFEFYNDRNVEKFIQIPWSEINEVDVSVSLKKWGRQFSIFTDTQGKVRFASK 84 (122)
T ss_pred hhcCeEEEcccceeecCCCChhheeEecHHHhheeheeehhhhhcceEEEEEcCCceEEEEeC
Confidence 3678999999999999988875 78899999999999999654
No 39
>PF02471 OspE: Borrelia outer surface protein E; InterPro: IPR003483 This is a family of outer surface proteins (Osp) from the Borrelia spp. spirochete []. The family includes OspE, OspF, and OspEF-related proteins (Erp) []. These proteins are coded for on different circular plasmids in the Borrelia genome.
Probab=25.61 E-value=56 Score=25.07 Aligned_cols=41 Identities=32% Similarity=0.477 Sum_probs=33.7
Q ss_pred CCeEeecCcEEeecccceEEcCCCeeecccceEEEeeceEE
Q 032363 81 GDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLV 121 (142)
Q Consensus 81 ~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V 121 (142)
.+...--|..+||.-.--+--|.||+.|..-|+|++++-.|
T Consensus 14 ~~nW~dLGtLvv~KeedgI~tgLN~~~GhsatfFsleesEv 54 (108)
T PF02471_consen 14 SGNWTDLGTLVVRKEEDGIETGLNVGGGHSATFFSLEESEV 54 (108)
T ss_pred CCCceeeeeEEEEeecCceeeccccCCCceEEEEEecHHHH
Confidence 45566678889998888899999999999999999986543
No 40
>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=23.70 E-value=51 Score=26.00 Aligned_cols=17 Identities=24% Similarity=0.405 Sum_probs=11.6
Q ss_pred eEeeCCeEeecCcEEee
Q 032363 77 VKIFGDQVAKPGAIIVR 93 (142)
Q Consensus 77 vK~~~Gq~V~~G~IIvR 93 (142)
+-+-+||+|++|++|++
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 44568999999999886
No 41
>COG5455 Predicted integral membrane protein [Function unknown]
Probab=23.08 E-value=82 Score=24.92 Aligned_cols=24 Identities=33% Similarity=0.578 Sum_probs=19.9
Q ss_pred ccceEEcCCCeeecccceEEEeeceEEEEE
Q 032363 95 RGTKFHPGKNVGLGKDHTIFSLIDGLVKFE 124 (142)
Q Consensus 95 RGtkfhPG~NVg~GrD~TLfAl~~G~V~F~ 124 (142)
||+.| |.+|-|+-|.+..+| |.|.
T Consensus 101 RGq~W-----vrvg~dyvLi~~~tG-lI~g 124 (129)
T COG5455 101 RGQHW-----VRVGGDYVLISDTTG-LIFG 124 (129)
T ss_pred CCcee-----EEECCeEEEEeecCc-eEEe
Confidence 46777 899999999999999 5553
No 42
>TIGR01015 hmgA homogentisate 1,2-dioxygenase. Missing in human disease alkaptonuria.
Probab=22.92 E-value=69 Score=29.63 Aligned_cols=20 Identities=35% Similarity=0.685 Sum_probs=16.8
Q ss_pred CCeEeecCcEEeecccceEE
Q 032363 81 GDQVAKPGAIIVRQRGTKFH 100 (142)
Q Consensus 81 ~Gq~V~~G~IIvRQRGtkfh 100 (142)
|--.|.||+|+|=|||++|.
T Consensus 166 G~L~v~pgei~VIPRG~~fr 185 (429)
T TIGR01015 166 GRLLVEPNEICVIPRGVRFR 185 (429)
T ss_pred cceEecCCCEEEecCccEEE
Confidence 33479999999999999775
No 43
>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=22.91 E-value=56 Score=22.67 Aligned_cols=20 Identities=20% Similarity=0.398 Sum_probs=14.9
Q ss_pred eEeeCCeEeecCcEEeeccc
Q 032363 77 VKIFGDQVAKPGAIIVRQRG 96 (142)
Q Consensus 77 vK~~~Gq~V~~G~IIvRQRG 96 (142)
+.+-+|+.|.||++|++=+|
T Consensus 49 ~~~~dG~~v~~g~~i~~i~G 68 (88)
T PF02749_consen 49 WLVKDGDRVEPGDVILEIEG 68 (88)
T ss_dssp ESS-TT-EEETTCEEEEEEE
T ss_pred EEeCCCCCccCCcEEEEEEe
Confidence 34479999999999998776
No 44
>PLN02658 homogentisate 1,2-dioxygenase
Probab=22.81 E-value=69 Score=29.68 Aligned_cols=21 Identities=38% Similarity=0.735 Sum_probs=17.3
Q ss_pred eCCeEeecCcEEeecccceEE
Q 032363 80 FGDQVAKPGAIIVRQRGTKFH 100 (142)
Q Consensus 80 ~~Gq~V~~G~IIvRQRGtkfh 100 (142)
+|--.|.||+|+|=|||++|.
T Consensus 164 fG~L~v~pgei~VIPRG~~fr 184 (435)
T PLN02658 164 LGKLQVSPGEIVVIPRGFRFA 184 (435)
T ss_pred ccceEecCCCEEEecCccEEE
Confidence 344578999999999999876
No 45
>TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit. The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria.
Probab=22.13 E-value=1.8e+02 Score=30.40 Aligned_cols=40 Identities=18% Similarity=0.173 Sum_probs=28.3
Q ss_pred ccceEEcCCCeeecccceEEEeeceEEEEEEeCCCceEEEEEec
Q 032363 95 RGTKFHPGKNVGLGKDHTIFSLIDGLVKFEKFGPDRKQVKYFAI 138 (142)
Q Consensus 95 RGtkfhPG~NVg~GrD~TLfAl~~G~V~F~k~~p~r~~V~V~p~ 138 (142)
.|.-+.||..|.. .|++...|.|+..+.+..++.+-|.|.
T Consensus 641 Ngq~I~aGTeIak----nI~SK~~GlVriikKn~i~reLiIkpG 680 (1227)
T TIGR02388 641 DGQYVEAGTEVVK----DIFCQNSGIVEVTQKNDILREIIVKPG 680 (1227)
T ss_pred CCCEeCCCCEEEE----eeeeccCcEEEEEeccceeEEEEEcCC
Confidence 3677777776664 599999999999865544566655553
No 46
>COG1726 NqrA Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrA [Energy production and conversion]
Probab=22.10 E-value=2e+02 Score=26.90 Aligned_cols=55 Identities=24% Similarity=0.385 Sum_probs=40.5
Q ss_pred CCCCCCccceeEeeCCeEeecCcEEeecccceEEcCCCeeecccceEEEeeceEEEEEEeCCCceE
Q 032363 67 GRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVKFEKFGPDRKQ 132 (142)
Q Consensus 67 GRdS~~KrLGvK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~F~k~~p~r~~ 132 (142)
|++=.|-|+++|+..|+.|++|++|+--. -.|| | -+-|+++|.|.=-..+.+|--
T Consensus 33 g~ey~gmrp~mkV~~gD~VkkGq~LfEdK---knpg--v------~~Tap~sG~V~aI~RG~KRvL 87 (447)
T COG1726 33 GEEYVGMRPSMKVREGDAVKKGQVLFEDK---KNPG--V------VFTAPVSGKVTAIHRGEKRVL 87 (447)
T ss_pred cccccCCCCcceeccCCeeeccceeeecc---cCCC--e------EEeccCCceEEEeecccceee
Confidence 56677889999999999999999998753 3444 2 245899999876444444433
No 47
>PF07177 Neuralized: Neuralized; InterPro: IPR006573 NEUZ is a domain of unknown function found in neuralized proteins, i.e. proteins involved in the specification of the neuroblast during cellular differentiation. ; PDB: 2YUE_A 2E63_A.
Probab=21.49 E-value=73 Score=21.76 Aligned_cols=19 Identities=53% Similarity=0.870 Sum_probs=11.9
Q ss_pred ceEEc---CCCeeecccceEEE
Q 032363 97 TKFHP---GKNVGLGKDHTIFS 115 (142)
Q Consensus 97 tkfhP---G~NVg~GrD~TLfA 115 (142)
.+||| |.||-+..|++.=.
T Consensus 2 l~FH~~~~G~nV~L~~~~~~A~ 23 (69)
T PF07177_consen 2 LRFHPNVHGKNVRLSNDGTVAR 23 (69)
T ss_dssp --EEC-EE-TTEEE-SSS-EEE
T ss_pred ccccCcccCCCEEEcCCCeEEE
Confidence 46998 99999999998544
No 48
>PF07370 DUF1489: Protein of unknown function (DUF1489); InterPro: IPR008320 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=21.31 E-value=65 Score=25.58 Aligned_cols=41 Identities=24% Similarity=0.227 Sum_probs=27.9
Q ss_pred EeecCcEEeecccceEEcCCCeeecccceEEEeeceEEEEEE
Q 032363 84 VAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVKFEK 125 (142)
Q Consensus 84 ~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~F~k 125 (142)
.|.+|.|.+||+=+.|.|-.. +=|..++.+=+.+-.|.-+.
T Consensus 52 WVikg~i~~RQ~Il~i~~~~~-~dG~~rc~ivL~P~li~v~~ 92 (137)
T PF07370_consen 52 WVIKGQIQCRQRILDIEEVTD-GDGIRRCAIVLDPELIRVEP 92 (137)
T ss_pred EEECCEEEEeeeeeeeeEecC-CCCcccEEEEECCcEEEccc
Confidence 599999999999888877432 11334566666666666543
No 49
>PRK01202 glycine cleavage system protein H; Provisional
Probab=20.89 E-value=1.2e+02 Score=22.82 Aligned_cols=31 Identities=19% Similarity=0.229 Sum_probs=20.5
Q ss_pred CeEeecCcEEeecccceEEcCCCeeecccceEEEeeceEEE
Q 032363 82 DQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLVK 122 (142)
Q Consensus 82 Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~ 122 (142)
|+.|.+|+.+..=...|. .++|+|+++|.|.
T Consensus 48 G~~v~~g~~~~~IEs~K~----------~~~i~sPvsG~Vv 78 (127)
T PRK01202 48 GDEVKAGETFGVVESVKA----------ASDIYAPVSGEVV 78 (127)
T ss_pred CCEecCCCEEEEEEEcce----------eeeeecCCCeEEE
Confidence 555555555555444333 4789999999985
No 50
>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed
Probab=20.39 E-value=1.4e+02 Score=31.33 Aligned_cols=45 Identities=18% Similarity=0.258 Sum_probs=31.7
Q ss_pred eEeeCCeEeecCcEEeecccceEEcCC---CeeecccceEEEeeceEEEEEEe
Q 032363 77 VKIFGDQVAKPGAIIVRQRGTKFHPGK---NVGLGKDHTIFSLIDGLVKFEKF 126 (142)
Q Consensus 77 vK~~~Gq~V~~G~IIvRQRGtkfhPG~---NVg~GrD~TLfAl~~G~V~F~k~ 126 (142)
+.+-+||+|++|++|+- |.|.. |+.-.--..|++-.+|.|+|+..
T Consensus 406 l~v~~g~~V~~~q~iae-----~~~~~~~~~~~e~~~~~i~s~~~G~v~~~~~ 453 (1364)
T CHL00117 406 LLVQNDQYVESEQVIAE-----IRAGTSTLNFKEKVRKHIYSDSEGEMHWSTD 453 (1364)
T ss_pred EEEeCcCEEcCCCEEEE-----ECCCCcccccccccceeEEEcCCcEEEcccc
Confidence 45678999999999884 55543 22222226799999999999763
Done!