Query 031785
Match_columns 153
No_of_seqs 124 out of 1032
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 05:18:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031785.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031785hhsearch_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 7.2E-47 1.6E-51 296.6 10.0 111 34-144 18-129 (144)
2 COG0211 RpmA Ribosomal protein 100.0 5.5E-47 1.2E-51 277.0 8.6 86 44-130 1-86 (87)
3 TIGR00062 L27 ribosomal protei 100.0 2.1E-45 4.5E-50 267.2 8.7 83 44-126 1-83 (83)
4 CHL00121 rpl27 ribosomal prote 100.0 2.8E-45 6.1E-50 268.0 9.1 85 44-129 1-85 (86)
5 PF01016 Ribosomal_L27: Riboso 100.0 2.3E-45 5E-50 265.7 7.6 81 45-126 1-81 (81)
6 PRK05435 rpmA 50S ribosomal pr 100.0 7.5E-45 1.6E-49 263.8 9.2 82 44-126 1-82 (82)
7 PF14382 ECR1_N: Exosome compl 95.6 0.03 6.6E-07 35.6 4.4 38 73-113 1-38 (39)
8 PRK09521 exosome complex RNA-b 95.3 0.048 1E-06 43.5 5.8 54 70-130 4-57 (189)
9 COG1096 Predicted RNA-binding 94.1 0.18 4E-06 42.0 6.5 60 69-135 3-62 (188)
10 PRK04163 exosome complex RNA-b 93.3 0.27 5.9E-06 40.8 6.2 54 68-131 5-58 (235)
11 PF03961 DUF342: Protein of un 89.5 1 2.2E-05 40.3 6.2 51 72-128 107-181 (451)
12 PF01551 Peptidase_M23: Peptid 85.7 1.9 4.2E-05 29.9 4.6 41 87-127 1-41 (96)
13 COG1315 Uncharacterized conser 78.2 2.2 4.7E-05 40.6 3.3 36 86-128 219-255 (543)
14 PRK14844 bifunctional DNA-dire 61.9 14 0.00029 41.5 5.2 64 66-130 2526-2602(2836)
15 PF13533 Biotin_lipoyl_2: Biot 61.7 7.4 0.00016 24.9 2.1 17 66-82 16-32 (50)
16 cd06850 biotinyl_domain The bi 55.9 29 0.00062 21.6 4.1 39 66-114 13-51 (67)
17 COG1097 RRP4 RNA-binding prote 54.6 28 0.0006 30.2 5.0 54 68-130 5-58 (239)
18 PRK09603 bifunctional DNA-dire 49.2 31 0.00067 39.0 5.3 65 66-131 2616-2694(2890)
19 TIGR02994 ectoine_eutE ectoine 46.3 28 0.00061 30.4 3.8 42 67-115 269-311 (325)
20 PF13375 RnfC_N: RnfC Barrel s 45.1 31 0.00067 25.6 3.4 34 68-112 46-79 (101)
21 PRK05889 putative acetyl-CoA c 41.1 44 0.00096 22.3 3.4 40 65-114 15-54 (71)
22 KOG3409 Exosomal 3'-5' exoribo 36.1 86 0.0019 26.6 5.0 62 72-136 6-67 (193)
23 cd06253 M14_ASTE_ASPA_like_3 A 33.2 69 0.0015 27.4 4.1 41 68-115 244-284 (298)
24 cd06663 Biotinyl_lipoyl_domain 29.7 87 0.0019 20.4 3.4 39 66-114 19-57 (73)
25 PRK13918 CRP/FNR family transc 29.6 2.4E+02 0.0051 21.3 6.2 23 100-122 27-49 (202)
26 PRK14875 acetoin dehydrogenase 29.1 75 0.0016 25.9 3.6 42 61-112 17-58 (371)
27 PF13540 RCC1_2: Regulator of 27.6 64 0.0014 18.6 2.1 20 94-113 4-23 (30)
28 PRK11637 AmiB activator; Provi 24.7 1.1E+02 0.0023 27.3 3.9 45 70-115 304-355 (428)
29 PF07290 DUF1449: Protein of u 24.5 1.4E+02 0.0031 24.8 4.5 27 106-133 152-178 (202)
30 COG4687 Uncharacterized protei 24.4 86 0.0019 24.9 3.0 41 75-115 23-84 (122)
31 PRK06549 acetyl-CoA carboxylas 24.3 1.1E+02 0.0024 23.8 3.5 43 60-112 69-111 (130)
32 PF02471 OspE: Borrelia outer 24.1 59 0.0013 25.2 1.9 41 70-110 14-54 (108)
33 PF02749 QRPTase_N: Quinolinat 23.2 57 0.0012 22.9 1.6 20 66-85 49-68 (88)
34 COG5455 Predicted integral mem 23.0 81 0.0018 25.2 2.6 24 84-113 101-124 (129)
35 PRK00807 50S ribosomal protein 22.8 84 0.0018 20.9 2.3 23 85-114 8-30 (52)
36 PRK08225 acetyl-CoA carboxylas 22.2 1.5E+02 0.0032 19.5 3.4 37 66-112 15-51 (70)
37 COG1724 Predicted RNA binding 21.9 46 0.001 23.8 0.9 8 78-85 21-28 (66)
38 PF07370 DUF1489: Protein of u 21.8 62 0.0013 26.0 1.7 52 73-125 52-106 (137)
39 PF00412 LIM: LIM domain; Int 21.2 75 0.0016 19.7 1.8 21 71-91 5-25 (58)
40 PF02911 Formyl_trans_C: Formy 20.9 2.8E+02 0.0061 18.8 5.1 35 90-124 57-91 (100)
41 cd06251 M14_ASTE_ASPA_like_1 A 20.3 1.4E+02 0.0031 25.1 3.7 40 68-115 234-273 (287)
No 1
>KOG4600 consensus Mitochondrial ribosomal protein MRP7 (L2) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.2e-47 Score=296.65 Aligned_cols=111 Identities=64% Similarity=1.079 Sum_probs=102.6
Q ss_pred CCCcceeeeeeeeecccccCCCCCCCCCcccceeeeCCeEeecCcEEeecccCeEeCCCCeeeeccceEEEeeceEEEEE
Q 031785 34 AGGLSLMFRRWATKKTAGSTKNGRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFE 113 (153)
Q Consensus 34 ~~~~~~~~~r~A~KK~~GStkNGRdS~~KrLGvK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~f~ 113 (153)
..++.++++||||||++|||+|||||+|+|||+|+|+||+|.||+||||||||+||||+|||||||||||||++|+|+|+
T Consensus 18 ss~~~~l~vR~AtKk~aGStKN~~dS~grrlGvKk~egq~V~~G~IIvrQRgtkfHPG~nVGiGKDhtifaL~eG~Vrf~ 97 (144)
T KOG4600|consen 18 SSGLSFLAVRWATKKGAGSTKNGRDSAGRRLGVKKYEGQSVIPGNIIVRQRGTKFHPGDNVGIGKDHTIFALEEGRVRFE 97 (144)
T ss_pred CCcceeeeeeeecccccCccccCCCCCcccccceecCCeeeecccEEEEecccccCCCcccccCCcceEEEeeccEEEEE
Confidence 34567889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EecC-CCceEEEeEeCCCCccccccccccccc
Q 031785 114 KHKL-SGRKWVHVEPKEGHVLHPLYANATANA 144 (153)
Q Consensus 114 ~~~~-~~rk~V~V~p~~~~~~~p~~~~~~~~~ 144 (153)
+++. +.||||+|+|..+..+||.+-++..-.
T Consensus 98 k~~~~~~Rk~i~V~~~~~~~l~~~~~k~~vr~ 129 (144)
T KOG4600|consen 98 KSKITPPRKWIGVDPRGGLPLPPPYYKATVRR 129 (144)
T ss_pred EccCCCCcceEEEeecCCccCCCccchhhhhh
Confidence 9865 459999999999999999887766544
No 2
>COG0211 RpmA Ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.5e-47 Score=276.97 Aligned_cols=86 Identities=63% Similarity=0.964 Sum_probs=83.3
Q ss_pred eeeecccccCCCCCCCCCcccceeeeCCeEeecCcEEeecccCeEeCCCCeeeeccceEEEeeceEEEEEEecCCCceEE
Q 031785 44 WATKKTAGSTKNGRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWV 123 (153)
Q Consensus 44 ~A~KK~~GStkNGRdS~~KrLGvK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~f~~~~~~~rk~V 123 (153)
|||||++|||+|||||++||||+|+++||.|.+|+||||||||+||||+|||+|+||||||+++|+|+|+... ++|+||
T Consensus 1 mA~KKg~GSt~NgRDS~~krLGvK~~~Gq~v~aG~IivRQRGTk~hpG~NVG~GkDhTlFAl~dG~Vkf~~k~-~~rk~v 79 (87)
T COG0211 1 MAHKKGGGSTRNGRDSESKRLGVKKFGGQFVKAGSIIVRQRGTKFHPGVNVGRGKDHTLFALVDGVVKFETKG-KNRKYV 79 (87)
T ss_pred CcccccccccccCccccccccceeeeCCeEEecccEEEEeccccccCCcccccCCCceEEEeeccEEEEEEcc-CCccEE
Confidence 6999999999999999999999999999999999999999999999999999999999999999999999985 799999
Q ss_pred EeEeCCC
Q 031785 124 HVEPKEG 130 (153)
Q Consensus 124 ~V~p~~~ 130 (153)
+|+|+..
T Consensus 80 sV~~~~~ 86 (87)
T COG0211 80 SVVPEAE 86 (87)
T ss_pred EEEeecc
Confidence 9999764
No 3
>TIGR00062 L27 ribosomal protein L27. Eubacterial, chloroplast, and mitochondrial. Mitochondrial members have an additional C-terminal domain.
Probab=100.00 E-value=2.1e-45 Score=267.22 Aligned_cols=83 Identities=66% Similarity=0.990 Sum_probs=80.5
Q ss_pred eeeecccccCCCCCCCCCcccceeeeCCeEeecCcEEeecccCeEeCCCCeeeeccceEEEeeceEEEEEEecCCCceEE
Q 031785 44 WATKKTAGSTKNGRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWV 123 (153)
Q Consensus 44 ~A~KK~~GStkNGRdS~~KrLGvK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~f~~~~~~~rk~V 123 (153)
|||||++|||+|||||+|||||+|+++||+|.||+||||||||+||||+||||||||||||+++|+|+|++++.++|+||
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 69999999999999999999999999999999999999999999999999999999999999999999999876789999
Q ss_pred EeE
Q 031785 124 HVE 126 (153)
Q Consensus 124 ~V~ 126 (153)
+|+
T Consensus 81 ~v~ 83 (83)
T TIGR00062 81 SVV 83 (83)
T ss_pred EEC
Confidence 984
No 4
>CHL00121 rpl27 ribosomal protein L27; Reviewed
Probab=100.00 E-value=2.8e-45 Score=267.98 Aligned_cols=85 Identities=60% Similarity=0.874 Sum_probs=81.5
Q ss_pred eeeecccccCCCCCCCCCcccceeeeCCeEeecCcEEeecccCeEeCCCCeeeeccceEEEeeceEEEEEEecCCCceEE
Q 031785 44 WATKKTAGSTKNGRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWV 123 (153)
Q Consensus 44 ~A~KK~~GStkNGRdS~~KrLGvK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~f~~~~~~~rk~V 123 (153)
|||||++|||+|||||+|||||+|+++||+|.||+||||||||+||||+||||||||||||+++|+|+|++. .+++++|
T Consensus 1 mA~KK~~GStkNgrdS~~KrLGvK~~~gq~V~~G~IivRQRGtk~hPG~NVg~GrD~TlfAl~~G~V~f~~~-~~~~~~v 79 (86)
T CHL00121 1 MAHKKGAGSTKNGRDSNAKRLGVKRFGGEKVSAGNILIRQRGTKFKPGLNVGCGKDFTLYALIDGFVKFKKK-NKKQKSI 79 (86)
T ss_pred CCcccccCcCCCCCCCCcccceeEEcCCEEEcCCcEEEEcCCCeECCCCcccccCCceEEEccceEEEEEEe-CCCCEEE
Confidence 699999999999999999999999999999999999999999999999999999999999999999999987 3689999
Q ss_pred EeEeCC
Q 031785 124 HVEPKE 129 (153)
Q Consensus 124 ~V~p~~ 129 (153)
+|+|..
T Consensus 80 sv~~~~ 85 (86)
T CHL00121 80 NVINIV 85 (86)
T ss_pred EEeecc
Confidence 999863
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=2.3e-45 Score=265.74 Aligned_cols=81 Identities=70% Similarity=1.100 Sum_probs=73.8
Q ss_pred eeecccccCCCCCCCCCcccceeeeCCeEeecCcEEeecccCeEeCCCCeeeeccceEEEeeceEEEEEEecCCCceEEE
Q 031785 45 ATKKTAGSTKNGRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVH 124 (153)
Q Consensus 45 A~KK~~GStkNGRdS~~KrLGvK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~f~~~~~~~rk~V~ 124 (153)
||||++|||+|||||+|||||||+++||+|.||+||||||||+||||+||||||||||||+++|+|+|+++ .++|+||+
T Consensus 1 A~KK~~GSt~NgrdS~~krlGvK~~~G~~V~~G~IivRQRgtk~hPG~NVg~GrD~TLfAl~~G~V~f~~~-~~~rk~v~ 79 (81)
T PF01016_consen 1 AHKKGGGSTKNGRDSNPKRLGVKKFGGQFVKAGNIIVRQRGTKFHPGENVGMGRDHTLFALVDGRVKFTKE-KRNRKYVS 79 (81)
T ss_dssp --SSSSSSSS--S-STTTTSEESSSTTCEESSTSEEEEBSSSSSEEBTTEEEETTSEEEESSSCEEEEEEE-TTTEEEEE
T ss_pred CCccccccccCCCCCCCcccEEEEeCCEEEcCCCEEEEeCCCcCcCCCCEEECCCCcEEEecCEEEEEEEe-CCCCEEEE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999 57899999
Q ss_pred eE
Q 031785 125 VE 126 (153)
Q Consensus 125 V~ 126 (153)
|+
T Consensus 80 V~ 81 (81)
T PF01016_consen 80 VV 81 (81)
T ss_dssp E-
T ss_pred eC
Confidence 95
No 6
>PRK05435 rpmA 50S ribosomal protein L27; Validated
Probab=100.00 E-value=7.5e-45 Score=263.81 Aligned_cols=82 Identities=65% Similarity=0.997 Sum_probs=79.2
Q ss_pred eeeecccccCCCCCCCCCcccceeeeCCeEeecCcEEeecccCeEeCCCCeeeeccceEEEeeceEEEEEEecCCCceEE
Q 031785 44 WATKKTAGSTKNGRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWV 123 (153)
Q Consensus 44 ~A~KK~~GStkNGRdS~~KrLGvK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~f~~~~~~~rk~V 123 (153)
|||||++|||+|||||+|||||+|+++||+|.||+||||||||+||||+||+|||||||||+++|+|+|++.. ++|++|
T Consensus 1 mA~KK~~GStkNgrdS~~krLGvK~~~g~~V~~G~IivRQRGtk~~PG~nVg~GrD~TlfA~~~G~V~f~~~~-~~~~~v 79 (82)
T PRK05435 1 MAHKKGGGSTRNGRDSESKRLGVKRFGGQFVKAGNIIVRQRGTKFHPGVNVGRGKDHTLFALVDGVVKFERKG-RNRKYV 79 (82)
T ss_pred CCcccccCcCCCCCCCCcccceeEecCCEEEcCCcEEEEeCCCeECCCCCEeecCCceEEEecceEEEEEEcC-CCcEEE
Confidence 6999999999999999999999999999999999999999999999999999999999999999999999874 689999
Q ss_pred EeE
Q 031785 124 HVE 126 (153)
Q Consensus 124 ~V~ 126 (153)
+|+
T Consensus 80 ~v~ 82 (82)
T PRK05435 80 SVV 82 (82)
T ss_pred EEC
Confidence 985
No 7
>PF14382 ECR1_N: Exosome complex exonuclease RRP4 N-terminal region; PDB: 2NN6_I 3M7N_C 2BA1_A 3M85_C.
Probab=95.57 E-value=0.03 Score=35.55 Aligned_cols=38 Identities=29% Similarity=0.547 Sum_probs=31.9
Q ss_pred EeecCcEEeecccCeEeCCCCeeeeccceEEEeeceEEEEE
Q 031785 73 RVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFE 113 (153)
Q Consensus 73 ~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~f~ 113 (153)
.|.||+.|-.. ..|.||.|+.+ +|..|||.+-|.|+..
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 48899999985 47899999999 9999999999999864
No 8
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=95.32 E-value=0.048 Score=43.48 Aligned_cols=54 Identities=22% Similarity=0.395 Sum_probs=43.6
Q ss_pred CCeEeecCcEEeecccCeEeCCCCeeeeccceEEEeeceEEEEEEecCCCceEEEeEeCCC
Q 031785 70 GGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVHVEPKEG 130 (153)
Q Consensus 70 ~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~f~~~~~~~rk~V~V~p~~~ 130 (153)
+++.|.||+.|.-. -.|.||.|+.. +|.+|||.+-|.+++..+ ++.|+|.|...
T Consensus 4 ~~~~V~PGe~l~~~--~e~~~G~Gty~-~~~~i~as~~G~~~id~~----~~~Isv~P~~~ 57 (189)
T PRK09521 4 QGDLVLPGDYLAVI--EEYLPGEGTYE-DNGEVYASVVGKVFIDDI----NRKISVIPFKK 57 (189)
T ss_pred cCCEECCCCccccc--cceEcCCCEEe-eCCEEEEEeeEEEEEcCC----CCEEEEecCcC
Confidence 67899999999754 36999999977 688899999999998543 45588877654
No 9
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=94.11 E-value=0.18 Score=42.03 Aligned_cols=60 Identities=22% Similarity=0.355 Sum_probs=48.9
Q ss_pred eCCeEeecCcEEeecccCeEeCCCCeeeeccceEEEeeceEEEEEEecCCCceEEEeEeCCCCcccc
Q 031785 69 FGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVHVEPKEGHVLHP 135 (153)
Q Consensus 69 ~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~f~~~~~~~rk~V~V~p~~~~~~~p 135 (153)
-+|.+|.||+.|..+ -.|.||+|+--= |+.|+|...|.+..+.+ .+.++|.|......+|
T Consensus 3 ~~g~~v~PGd~~a~~--EE~~~G~gt~~~-~g~i~Aa~~G~~~~d~~----n~~~~V~p~~~~~~~~ 62 (188)
T COG1096 3 KDGTFVLPGDVLAVI--EEFLPGEGTYEE-GGEIRAAATGVVRRDDK----NRVISVKPGKKTPPLP 62 (188)
T ss_pred ccCcEEcCcceeeee--eeeecCCCeEeE-CCEEEEeecccEEEccc----ceEEEeccCCCCCCCC
Confidence 468899999999975 479999999876 99999999999988753 5678888877644444
No 10
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=93.26 E-value=0.27 Score=40.82 Aligned_cols=54 Identities=24% Similarity=0.392 Sum_probs=42.6
Q ss_pred eeCCeEeecCcEEeecccCeEeCCCCeeeeccceEEEeeceEEEEEEecCCCceEEEeEeCCCC
Q 031785 68 KFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVHVEPKEGH 131 (153)
Q Consensus 68 ~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~f~~~~~~~rk~V~V~p~~~~ 131 (153)
..++..|.||+.|.- -.|.||.|+.. +|..|+|.+-|.+.+.. +.|+|.|....
T Consensus 5 ~~~~~~V~PGd~l~~---~~~~~G~Gty~-~~g~i~As~~G~~~~~~------~~i~V~p~~~~ 58 (235)
T PRK04163 5 VEDRKIVVPGDLLAE---GEFKAGRGTYK-ENGKIYSTVVGLVDIKD------DKVRVIPLEGK 58 (235)
T ss_pred eeCCcEECCCCCcCc---CCeecCCceEE-eCCEEEEEEeEEEEEEC------CEEEEEECCCc
Confidence 346789999999952 36999999987 89999999999999753 26788775543
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=89.53 E-value=1 Score=40.28 Aligned_cols=51 Identities=29% Similarity=0.562 Sum_probs=39.7
Q ss_pred eEeecCcEEee----ccc------------------CeEeCCCCeeee-cc-ceEEEeeceEEEEEEecCCCceEEEeEe
Q 031785 72 ERVIPGNIIVR----QRG------------------TRFHPGDYVGMG-KD-HTLYALKEGRVKFEKHKLSGRKWVHVEP 127 (153)
Q Consensus 72 q~V~~G~IIvR----QRG------------------tkfhPG~NVg~G-rD-~TLfAl~~G~V~f~~~~~~~rk~V~V~p 127 (153)
..|.+|+.|++ +.| ..|.+|+||.+- .| .+|+|.++|++.|.... ++|.|
T Consensus 107 ~~V~~G~~la~~~p~~~G~~G~~V~G~~I~~~~~~~~~~~~g~~~~~~~~d~~~~~A~~~G~~~~~~~~------i~V~~ 180 (451)
T PF03961_consen 107 PSVKKGDVLAEKIPPTPGEPGRDVFGEPIPAKPGKDIPLKAGKNTEVSEEDGNKLYAAIDGRPVFENGK------ISVDP 180 (451)
T ss_pred eEECCCCEEEEEccCCCCCCCcccCCCCcCCCCCCccceeCCCCEEEEcCCCCEEEEecCCEEEEECCE------EEEEE
Confidence 34888888887 334 478899999999 77 57999999999999542 66666
Q ss_pred C
Q 031785 128 K 128 (153)
Q Consensus 128 ~ 128 (153)
.
T Consensus 181 ~ 181 (451)
T PF03961_consen 181 V 181 (451)
T ss_pred e
Confidence 4
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=85.75 E-value=1.9 Score=29.88 Aligned_cols=41 Identities=24% Similarity=0.383 Sum_probs=28.8
Q ss_pred eEeCCCCeeeeccceEEEeeceEEEEEEecCCCceEEEeEe
Q 031785 87 RFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVHVEP 127 (153)
Q Consensus 87 kfhPG~NVg~GrD~TLfAl~~G~V~f~~~~~~~rk~V~V~p 127 (153)
+||.|--+.......++|+.+|+|.|.......-.+|-|.-
T Consensus 1 r~h~Gid~~~~~g~~V~A~~~G~V~~~~~~~~~g~~V~i~~ 41 (96)
T PF01551_consen 1 RFHNGIDFAAPEGTPVYAPADGKVVFVGEDPGYGNYVIIQH 41 (96)
T ss_dssp -EE-SEEEEETTT-EEEESSSEEEEEEEEETTTEEEEEEEE
T ss_pred CCeeeEEeCCCCCCEEEeCccEEEEEEEeccCCccEEEEEe
Confidence 47888777777778899999999999886433455565554
No 13
>COG1315 Uncharacterized conserved protein [Function unknown]
Probab=78.16 E-value=2.2 Score=40.64 Aligned_cols=36 Identities=28% Similarity=0.360 Sum_probs=29.6
Q ss_pred CeEeCCCCeeeecc-ceEEEeeceEEEEEEecCCCceEEEeEeC
Q 031785 86 TRFHPGDYVGMGKD-HTLYALKEGRVKFEKHKLSGRKWVHVEPK 128 (153)
Q Consensus 86 tkfhPG~NVg~GrD-~TLfAl~~G~V~f~~~~~~~rk~V~V~p~ 128 (153)
..+++|+|+- -|| .||.|.++|.+-+.+. .|+|+|.
T Consensus 219 ~~l~lG~nt~-~kd~~tlvA~~~G~~~~s~~------tI~V~~i 255 (543)
T COG1315 219 IKLNLGKNTA-FKDNNTLVAKRDGQPIVSKN------TISVYPI 255 (543)
T ss_pred eeeecCCCCc-cCCCCEEEEeeCCeEEecCC------eeEEEEE
Confidence 5899999999 666 8999999999988654 3777764
No 14
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=61.85 E-value=14 Score=41.49 Aligned_cols=64 Identities=23% Similarity=0.431 Sum_probs=42.8
Q ss_pred eeeeCCeEeecCcEEee-cccC----eEeCCC-------CeeeeccceEEEeeceEEEEE-EecCCCceEEEeEeCCC
Q 031785 66 VKKFGGERVIPGNIIVR-QRGT----RFHPGD-------YVGMGKDHTLYALKEGRVKFE-KHKLSGRKWVHVEPKEG 130 (153)
Q Consensus 66 vK~~~Gq~V~~G~IIvR-QRGt----kfhPG~-------NVg~GrD~TLfAl~~G~V~f~-~~~~~~rk~V~V~p~~~ 130 (153)
+=+.+||.|.+|+||+| -|-+ -+--|. -...-+|+.+.|.++|+|.|- ++ .++++.|-|.++++
T Consensus 2526 l~v~~g~~v~~Gdilakipr~~~~t~DIT~GLpRv~eLFEar~pk~~a~isei~G~V~~~~~~-~~~~~~i~i~~~~~ 2602 (2836)
T PRK14844 2526 LNVQDGQKVHAGDVITRTPRESVKTRDITGGLPRVIELFEARRPKEHAIVSEIDGYVAFSEKD-RRGKRSILIKPVDE 2602 (2836)
T ss_pred EeeccCceecccceeecccccccccCccCCCCccchheeeeecCCCceEEecCCcEEEecccc-cCCceEEEEECCCC
Confidence 34679999999999999 2221 111221 123567899999999999993 22 24566788888664
No 15
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=61.65 E-value=7.4 Score=24.95 Aligned_cols=17 Identities=24% Similarity=0.403 Sum_probs=14.8
Q ss_pred eeeeCCeEeecCcEEee
Q 031785 66 VKKFGGERVIPGNIIVR 82 (153)
Q Consensus 66 vK~~~Gq~V~~G~IIvR 82 (153)
+..-.|++|.+|++|++
T Consensus 16 v~V~~G~~VkkGd~L~~ 32 (50)
T PF13533_consen 16 VYVKEGQQVKKGDVLLV 32 (50)
T ss_pred EEecCCCEEcCCCEEEE
Confidence 45669999999999987
No 16
>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=55.90 E-value=29 Score=21.58 Aligned_cols=39 Identities=21% Similarity=0.129 Sum_probs=29.5
Q ss_pred eeeeCCeEeecCcEEeecccCeEeCCCCeeeeccceEEEeeceEEEEEE
Q 031785 66 VKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEK 114 (153)
Q Consensus 66 vK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~f~~ 114 (153)
+..-.|++|.+|+.|.+=... ..+..|.|+.+|+|..-.
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 566789999999999963321 125789999999997654
No 17
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=54.65 E-value=28 Score=30.18 Aligned_cols=54 Identities=20% Similarity=0.346 Sum_probs=38.4
Q ss_pred eeCCeEeecCcEEeecccCeEeCCCCeeeeccceEEEeeceEEEEEEecCCCceEEEeEeCCC
Q 031785 68 KFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVHVEPKEG 130 (153)
Q Consensus 68 ~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~f~~~~~~~rk~V~V~p~~~ 130 (153)
....+.|.||+++.-+- .+..|.++.+ +|.-+||.+-|.|..+.+. |.|.|.++
T Consensus 5 ~~~~~iV~PGd~vl~~~--~~~~G~Gty~-~~~~iyssv~G~~~~~~~~------v~VIpl~g 58 (239)
T COG1097 5 VSMRKIVLPGDLVLAEG--SYKLGHGTYF-EGGKIYSSVVGLLDVKGKL------VRVIPLEG 58 (239)
T ss_pred ccccceecCCCccCCCC--CEecCCCcEe-cCCEEEEEEEeEEEEeCCE------EEEEeCCC
Confidence 35678899999654332 3555555555 9999999999999987642 66766554
No 18
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=49.18 E-value=31 Score=39.00 Aligned_cols=65 Identities=20% Similarity=0.320 Sum_probs=43.8
Q ss_pred eeeeCCeEeecCcEEee-cccCe----EeCCC-------Cee--eeccceEEEeeceEEEEEEecCCCceEEEeEeCCCC
Q 031785 66 VKKFGGERVIPGNIIVR-QRGTR----FHPGD-------YVG--MGKDHTLYALKEGRVKFEKHKLSGRKWVHVEPKEGH 131 (153)
Q Consensus 66 vK~~~Gq~V~~G~IIvR-QRGtk----fhPG~-------NVg--~GrD~TLfAl~~G~V~f~~~~~~~rk~V~V~p~~~~ 131 (153)
+=..+|+.|.+|+||+| .|-+- +--|. -.. .-+|..+.|.++|+|+|.++ .+.++.|.|.+++++
T Consensus 2616 l~v~~g~~v~~gdilak~p~~~~~t~DITgGLprv~eLfear~~~pk~~a~i~ei~G~v~~~~~-~~~~~~i~i~~~~~~ 2694 (2890)
T PRK09603 2616 IAISDGSSVEQAEVLAKIPKATVKSRDITGGLPRVSELFEARKPKPKDVAILSEVDGIVSFGKP-IRNKEHIIVTSKDGR 2694 (2890)
T ss_pred EEecCCCEecccceEeeccccccccccccCCcccchhheEeecCCCCCceEEeccceEEEeccc-cCCceEEEEECCCCc
Confidence 34678999999999998 44321 11111 012 34689999999999999654 245677888887654
No 19
>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=46.26 E-value=28 Score=30.41 Aligned_cols=42 Identities=19% Similarity=0.141 Sum_probs=30.6
Q ss_pred eeeCCeEeecCcEEeecccCeEe-CCCCeeeeccceEEEeeceEEEEEEe
Q 031785 67 KKFGGERVIPGNIIVRQRGTRFH-PGDYVGMGKDHTLYALKEGRVKFEKH 115 (153)
Q Consensus 67 K~~~Gq~V~~G~IIvRQRGtkfh-PG~NVg~GrD~TLfAl~~G~V~f~~~ 115 (153)
++--|+.|.+|++|.+..- +. +|+-+ +++.|+.+|+|-+.+.
T Consensus 269 ~v~~G~~V~~G~~lg~I~d--~~~~G~~~-----~~i~Ap~dGiV~~~~~ 311 (325)
T TIGR02994 269 MIDLGDPVSKGDVIARVYP--VGRTGVAP-----VEYRAKRDGLLAARHF 311 (325)
T ss_pred ecCCCCEeCCCCEEEEEEC--CCCCCCce-----EEEEeCCCcEEEEEeC
Confidence 3445889999999888764 22 44333 6899999999988664
No 20
>PF13375 RnfC_N: RnfC Barrel sandwich hybrid domain
Probab=45.11 E-value=31 Score=25.57 Aligned_cols=34 Identities=24% Similarity=0.317 Sum_probs=25.0
Q ss_pred eeCCeEeecCcEEeecccCeEeCCCCeeeeccceEEEeeceEEEE
Q 031785 68 KFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKF 112 (153)
Q Consensus 68 ~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~f 112 (153)
.--||+|..|++|.+-.|. + .-.|+|.++|.|.=
T Consensus 46 V~~Gd~V~~GQ~Ia~~~~~-------~----sa~iHAsvSG~V~~ 79 (101)
T PF13375_consen 46 VKVGDKVKKGQLIAEAEGF-------L----SAPIHASVSGTVTA 79 (101)
T ss_pred EcCCCEEcCCCEEEecCCC-------c----EeeEEcCCCeEEEE
Confidence 4468999999999886541 1 12689999999953
No 21
>PRK05889 putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Provisional
Probab=41.07 E-value=44 Score=22.29 Aligned_cols=40 Identities=18% Similarity=0.179 Sum_probs=29.1
Q ss_pred ceeeeCCeEeecCcEEeecccCeEeCCCCeeeeccceEEEeeceEEEEEE
Q 031785 65 GVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEK 114 (153)
Q Consensus 65 GvK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~f~~ 114 (153)
=+.+-.|+.|.+|+.|+-=--.| -++.|.|..+|+|.-..
T Consensus 15 ~~~v~~Gd~V~~g~~l~~ve~~K----------~~~~I~a~~~G~V~~i~ 54 (71)
T PRK05889 15 EVVVNEGDQIGKGDTLVLLESMK----------MEIPVLAEVAGTVSKVS 54 (71)
T ss_pred EEEeCCCCEECCCCEEEEEEecc----------ceeEEeCCCCEEEEEEE
Confidence 36777899999999998322222 36789999999986443
No 22
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=36.09 E-value=86 Score=26.57 Aligned_cols=62 Identities=23% Similarity=0.366 Sum_probs=39.7
Q ss_pred eEeecCcEEeecccCeEeCCCCeeeeccceEEEeeceEEEEEEecCCCceEEEeEeCCCCccccc
Q 031785 72 ERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVHVEPKEGHVLHPL 136 (153)
Q Consensus 72 q~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~f~~~~~~~rk~V~V~p~~~~~~~p~ 136 (153)
-+|.||+.+.|--+- ..+|++..- +...|||...|.+ |-..-..+++.+++.-....+++|-
T Consensus 6 ~~~lpG~~~c~~e~~-~~~g~Gtye-~~~yI~aS~ag~~-~~~~~~~~~~v~~~~~~~~~~~LP~ 67 (193)
T KOG3409|consen 6 TLVLPGEVVCRAEGE-YRMGEGTYE-RNGYIFASVAGVN-FRDNLVQKIEVVSVEKQLFNELLPF 67 (193)
T ss_pred EEEcccceeeecccc-cccccceee-cCCeEEeccccce-eecCCccceeeeeecccchhhcCCc
Confidence 367888888876652 367777654 3458999999955 4333234566666665555555554
No 23
>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=33.16 E-value=69 Score=27.43 Aligned_cols=41 Identities=20% Similarity=0.216 Sum_probs=28.8
Q ss_pred eeCCeEeecCcEEeecccCeEeCCCCeeeeccceEEEeeceEEEEEEe
Q 031785 68 KFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKH 115 (153)
Q Consensus 68 ~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~f~~~ 115 (153)
+--|+.|.+|++|.+..=. ++|+-+ +++.|+.+|+|-+.+.
T Consensus 244 ~~~G~~V~~Gq~lg~i~dp--~~g~~~-----~~v~Ap~dGiv~~~~~ 284 (298)
T cd06253 244 KHLGDIVKRGDVIGEIVDP--LEGEVI-----EEVIAPCDGILFTLRE 284 (298)
T ss_pred cCCCCEECCCCEEEEEeCC--CCCCee-----EEEEcCCCeEEEEeec
Confidence 4457888888888776542 223222 5899999999998765
No 24
>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=29.74 E-value=87 Score=20.39 Aligned_cols=39 Identities=23% Similarity=0.246 Sum_probs=27.5
Q ss_pred eeeeCCeEeecCcEEeecccCeEeCCCCeeeeccceEEEeeceEEEEEE
Q 031785 66 VKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEK 114 (153)
Q Consensus 66 vK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~f~~ 114 (153)
+..-.|+.|.+|+.|..=-..| -...|.|+.+|.|.-..
T Consensus 19 ~~v~~G~~v~~g~~l~~ie~~k----------~~~~i~ap~~G~v~~~~ 57 (73)
T cd06663 19 WLKKVGDKVKKGDVLAEIEAMK----------ATSDVEAPKSGTVKKVL 57 (73)
T ss_pred EEcCCcCEECCCCEEEEEEeCC----------eEEEEEcCCCEEEEEEE
Confidence 5566888888888888632221 25679999999986543
No 25
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=29.59 E-value=2.4e+02 Score=21.29 Aligned_cols=23 Identities=22% Similarity=0.424 Sum_probs=17.4
Q ss_pred ceEEEeeceEEEEEEecCCCceE
Q 031785 100 HTLYALKEGRVKFEKHKLSGRKW 122 (153)
Q Consensus 100 ~TLfAl~~G~V~f~~~~~~~rk~ 122 (153)
+.+|-+.+|.|+.++....++..
T Consensus 27 ~~~y~I~~G~vr~~~~~~~G~e~ 49 (202)
T PRK13918 27 DMLYRVRSGLVRLHTVDDEGNAL 49 (202)
T ss_pred CeEEEEEeeEEEEEEECCCCCEE
Confidence 67999999999998864444433
No 26
>PRK14875 acetoin dehydrogenase E2 subunit dihydrolipoyllysine-residue acetyltransferase; Provisional
Probab=29.06 E-value=75 Score=25.91 Aligned_cols=42 Identities=17% Similarity=0.116 Sum_probs=30.8
Q ss_pred CcccceeeeCCeEeecCcEEeecccCeEeCCCCeeeeccceEEEeeceEEEE
Q 031785 61 PKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKF 112 (153)
Q Consensus 61 ~KrLGvK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~f 112 (153)
++=.-+.+-.|+.|.+|++|+.--. +--.+.+-|+.+|+|.-
T Consensus 17 g~~~~~~~~~g~~v~~~~~~~~~e~----------~k~~~~~~a~~~g~~~~ 58 (371)
T PRK14875 17 GKVAGWLVQEGDEVEKGDELLDVET----------DKITNEVEAPAAGTLRR 58 (371)
T ss_pred EEEEEEEcCCCCEeCCCCEEEEEEe----------cceeEEEecCCCeEEEE
Confidence 4455577889999999999987221 22347799999999863
No 27
>PF13540 RCC1_2: Regulator of chromosome condensation (RCC1) repeat; PDB: 3QI0_D 1JTD_B 3QHY_B.
Probab=27.61 E-value=64 Score=18.62 Aligned_cols=20 Identities=25% Similarity=0.230 Sum_probs=15.8
Q ss_pred eeeeccceEEEeeceEEEEE
Q 031785 94 VGMGKDHTLYALKEGRVKFE 113 (153)
Q Consensus 94 Vg~GrD~TLfAl~~G~V~f~ 113 (153)
|-.|.+||+.=+.+|.|.--
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 66899999999999998543
No 28
>PRK11637 AmiB activator; Provisional
Probab=24.72 E-value=1.1e+02 Score=27.27 Aligned_cols=45 Identities=22% Similarity=0.463 Sum_probs=27.3
Q ss_pred CCeEeec--CcEEeecccCeE-----eCCCCeeeeccceEEEeeceEEEEEEe
Q 031785 70 GGERVIP--GNIIVRQRGTRF-----HPGDYVGMGKDHTLYALKEGRVKFEKH 115 (153)
Q Consensus 70 ~Gq~V~~--G~IIvRQRGtkf-----hPG~NVg~GrD~TLfAl~~G~V~f~~~ 115 (153)
.|.+.+| |.|+ ..=|... |.|--..-..+-.++|..+|+|.|...
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 3334433 344444444567899999999999743
No 29
>PF07290 DUF1449: Protein of unknown function (DUF1449); InterPro: IPR010840 This family consists of several bacterial proteins of around 210 residues in length. The function of this family is unknown.
Probab=24.46 E-value=1.4e+02 Score=24.83 Aligned_cols=27 Identities=19% Similarity=0.449 Sum_probs=21.2
Q ss_pred eceEEEEEEecCCCceEEEeEeCCCCcc
Q 031785 106 KEGRVKFEKHKLSGRKWVHVEPKEGHVL 133 (153)
Q Consensus 106 ~~G~V~f~~~~~~~rk~V~V~p~~~~~~ 133 (153)
.+|.|++..+ +.++.||.|.|++++++
T Consensus 152 ~~aqa~V~D~-~Gq~hyv~veP~~~~~~ 178 (202)
T PF07290_consen 152 SPAQARVKDQ-FGQLHYVMVEPEAGEEF 178 (202)
T ss_pred CceEEEEEec-CCCEEEEEEeeCCCCCC
Confidence 4688888876 57899999999966544
No 30
>COG4687 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.41 E-value=86 Score=24.87 Aligned_cols=41 Identities=22% Similarity=0.519 Sum_probs=36.2
Q ss_pred ecCcEEeecccCeEeCCCCee---------------------eeccceEEEeeceEEEEEEe
Q 031785 75 IPGNIIVRQRGTRFHPGDYVG---------------------MGKDHTLYALKEGRVKFEKH 115 (153)
Q Consensus 75 ~~G~IIvRQRGtkfhPG~NVg---------------------~GrD~TLfAl~~G~V~f~~~ 115 (153)
.-|.||+=..|+.|++--||. +||.+.|+-...|.|.|..+
T Consensus 23 ~~GkiliGDkgfEFYn~~nv~k~iqipWs~i~~v~vsvs~KK~~~~f~i~td~~gk~~FaSk 84 (122)
T COG4687 23 EYGKILIGDKGFEFYNDRNVEKFIQIPWSEINEVDVSVSLKKWGRQFSIFTDTQGKVRFASK 84 (122)
T ss_pred hcCeEEEcccceeecCCCChhheeEecHHHhheeheeehhhhhcceEEEEEcCCceEEEEeC
Confidence 568899999999999988874 78899999999999999865
No 31
>PRK06549 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=24.31 E-value=1.1e+02 Score=23.80 Aligned_cols=43 Identities=16% Similarity=0.175 Sum_probs=33.4
Q ss_pred CCcccceeeeCCeEeecCcEEeecccCeEeCCCCeeeeccceEEEeeceEEEE
Q 031785 60 KPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKF 112 (153)
Q Consensus 60 ~~KrLGvK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~f 112 (153)
.++=+=+....|+.|..|+.|+.=.-.|. ...|.|..+|+|..
T Consensus 69 ~G~V~~i~V~~Gd~V~~Gq~L~~lEamKm----------e~eI~Ap~~G~V~~ 111 (130)
T PRK06549 69 PGTILKVLVAVGDQVTENQPLLILEAMKM----------ENEIVASSAGTVTA 111 (130)
T ss_pred CEEEEEEEeCCCCEECCCCEEEEEeccCc----------cEEEEcCCCeEEEE
Confidence 34555688899999999999987544442 57899999999964
No 32
>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=24.08 E-value=59 Score=25.21 Aligned_cols=41 Identities=29% Similarity=0.499 Sum_probs=33.3
Q ss_pred CCeEeecCcEEeecccCeEeCCCCeeeeccceEEEeeceEE
Q 031785 70 GGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRV 110 (153)
Q Consensus 70 ~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V 110 (153)
.+...--|.++||.-.--+--|.||+.|..-|+|++.+-.|
T Consensus 14 ~~nW~dLGtLvv~KeedgI~tgLN~~~GhsatfFsleesEv 54 (108)
T PF02471_consen 14 SGNWTDLGTLVVRKEEDGIETGLNVGGGHSATFFSLEESEV 54 (108)
T ss_pred CCCceeeeeEEEEeecCceeeccccCCCceEEEEEecHHHH
Confidence 45566667888888888899999999999999999876544
No 33
>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=23.17 E-value=57 Score=22.92 Aligned_cols=20 Identities=35% Similarity=0.599 Sum_probs=15.2
Q ss_pred eeeeCCeEeecCcEEeeccc
Q 031785 66 VKKFGGERVIPGNIIVRQRG 85 (153)
Q Consensus 66 vK~~~Gq~V~~G~IIvRQRG 85 (153)
+..-||+.|.+|++|++=+|
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 34579999999999998777
No 34
>COG5455 Predicted integral membrane protein [Function unknown]
Probab=23.02 E-value=81 Score=25.21 Aligned_cols=24 Identities=33% Similarity=0.562 Sum_probs=19.6
Q ss_pred ccCeEeCCCCeeeeccceEEEeeceEEEEE
Q 031785 84 RGTRFHPGDYVGMGKDHTLYALKEGRVKFE 113 (153)
Q Consensus 84 RGtkfhPG~NVg~GrD~TLfAl~~G~V~f~ 113 (153)
||+.| |.+|-|+-|.+..+| |-|-
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 45566 899999999999999 5554
No 35
>PRK00807 50S ribosomal protein L24e; Validated
Probab=22.78 E-value=84 Score=20.86 Aligned_cols=23 Identities=26% Similarity=0.541 Sum_probs=16.1
Q ss_pred cCeEeCCCCeeeeccceEEEeeceEEEEEE
Q 031785 85 GTRFHPGDYVGMGKDHTLYALKEGRVKFEK 114 (153)
Q Consensus 85 GtkfhPG~NVg~GrD~TLfAl~~G~V~f~~ 114 (153)
|.+++||.+. .|-..||.|-|..
T Consensus 8 G~~I~pg~G~-------~~vr~Dgkv~~Fc 30 (52)
T PRK00807 8 GKEIEPGTGK-------MYVKKDGTILYFC 30 (52)
T ss_pred CCeEcCCCCe-------EEEEeCCcEEEEe
Confidence 7788999874 4566677776654
No 36
>PRK08225 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=22.24 E-value=1.5e+02 Score=19.50 Aligned_cols=37 Identities=22% Similarity=0.206 Sum_probs=27.0
Q ss_pred eeeeCCeEeecCcEEeecccCeEeCCCCeeeeccceEEEeeceEEEE
Q 031785 66 VKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKF 112 (153)
Q Consensus 66 vK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~f 112 (153)
+..-.|+.|.+|+.|..=.-.| -...+.|..+|+|.-
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 5666789999999888733222 267799999998853
No 37
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=21.90 E-value=46 Score=23.85 Aligned_cols=8 Identities=50% Similarity=0.746 Sum_probs=4.8
Q ss_pred cEEeeccc
Q 031785 78 NIIVRQRG 85 (153)
Q Consensus 78 ~IIvRQRG 85 (153)
=-++||+|
T Consensus 21 f~~vrqkG 28 (66)
T COG1724 21 FQLVRQKG 28 (66)
T ss_pred cEEEEeec
Confidence 34566666
No 38
>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=21.77 E-value=62 Score=25.99 Aligned_cols=52 Identities=21% Similarity=0.233 Sum_probs=33.2
Q ss_pred EeecCcEEeecccCeEeCCCCeeeeccceEEEeeceEEEEEEe---cCCCceEEEe
Q 031785 73 RVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKH---KLSGRKWVHV 125 (153)
Q Consensus 73 ~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~f~~~---~~~~rk~V~V 125 (153)
.|+.|.|.+||+-+.|.|-..= =|..++.+=+.+-.|..... +|..=+|..-
T Consensus 52 WVikg~i~~RQ~Il~i~~~~~~-dG~~rc~ivL~P~li~v~~~p~RpFQGWRYL~~ 106 (137)
T PF07370_consen 52 WVIKGQIQCRQRILDIEEVTDG-DGIRRCAIVLDPELIRVEPRPRRPFQGWRYLKP 106 (137)
T ss_pred EEECCEEEEeeeeeeeeEecCC-CCcccEEEEECCcEEEcccccCCCCCccccCCc
Confidence 6999999999999888774321 13335666666666666543 3444555443
No 39
>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=21.18 E-value=75 Score=19.66 Aligned_cols=21 Identities=24% Similarity=0.610 Sum_probs=17.2
Q ss_pred CeEeecCcEEeecccCeEeCC
Q 031785 71 GERVIPGNIIVRQRGTRFHPG 91 (153)
Q Consensus 71 Gq~V~~G~IIvRQRGtkfhPG 91 (153)
++.|.++.++++..|..|||-
T Consensus 5 ~~~I~~~~~~~~~~~~~~H~~ 25 (58)
T PF00412_consen 5 GKPIYGTEIVIKAMGKFWHPE 25 (58)
T ss_dssp SSBESSSSEEEEETTEEEETT
T ss_pred CCCccCcEEEEEeCCcEEEcc
Confidence 456778888888899999985
No 40
>PF02911 Formyl_trans_C: Formyl transferase, C-terminal domain; InterPro: IPR005793 Methionyl-tRNA formyltransferase (2.1.2.9 from EC) transfers a formyl group onto the amino terminus of the acyl moiety of the methionyl aminoacyl-tRNA. The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and by impairing its binding to EFTU-GTP. This family also includes formyltetrahydrofolate dehydrogenases, which produce formate from formyl-tetrahydrofolate. These enzymes contain an N-terminal domain in common with other formyl transferase enzymes (IPR002376 from INTERPRO). The C-terminal domain has an open beta-barrel fold [].; GO: 0016742 hydroxymethyl-, formyl- and related transferase activity, 0009058 biosynthetic process; PDB: 3RFO_D 1Z7E_C 2BLN_A 1YRW_A 1FMT_A 2FMT_B 3Q0I_A 3R8X_A 3TQQ_A 2BW0_A ....
Probab=20.95 E-value=2.8e+02 Score=18.85 Aligned_cols=35 Identities=26% Similarity=0.412 Sum_probs=24.7
Q ss_pred CCCCeeeeccceEEEeeceEEEEEEecCCCceEEE
Q 031785 90 PGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVH 124 (153)
Q Consensus 90 PG~NVg~GrD~TLfAl~~G~V~f~~~~~~~rk~V~ 124 (153)
||+=+.+..+.=+++..+|.|....-...+++-++
T Consensus 57 pG~i~~~~~~~l~V~~~dg~l~i~~~q~~gkk~~~ 91 (100)
T PF02911_consen 57 PGTIVYIDKNGLLVACGDGALRIRELQPEGKKPMS 91 (100)
T ss_dssp TTBEEEEETTEEEEETSBSEEEEEEEEETTS-EEE
T ss_pred CceEEEEcCCEEEEEECCcEEEEEEEEcCCCCEEe
Confidence 88777777777788888999988765444555443
No 41
>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=20.26 E-value=1.4e+02 Score=25.14 Aligned_cols=40 Identities=18% Similarity=0.178 Sum_probs=27.6
Q ss_pred eeCCeEeecCcEEeecccCeEeCCCCeeeeccceEEEeeceEEEEEEe
Q 031785 68 KFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKH 115 (153)
Q Consensus 68 ~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrD~TLfAl~~G~V~f~~~ 115 (153)
+--|+.|.+|++|.+..-. -| ....++.|+.+|.|.+.+.
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 4457888888888776431 11 1127899999999977654
Done!