Query 033652
Match_columns 114
No_of_seqs 107 out of 1026
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 04:44:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033652.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033652hhsearch_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 3E-49 6.5E-54 276.5 8.8 86 5-91 1-86 (87)
2 KOG4600 Mitochondrial ribosoma 100.0 1.9E-47 4.2E-52 286.9 9.2 106 1-106 24-130 (144)
3 CHL00121 rpl27 ribosomal prote 100.0 2.6E-47 5.6E-52 266.7 9.1 84 5-89 1-84 (86)
4 TIGR00062 L27 ribosomal protei 100.0 3.3E-47 7.2E-52 264.7 8.8 83 5-87 1-83 (83)
5 PF01016 Ribosomal_L27: Riboso 100.0 2.8E-47 6.1E-52 263.9 7.2 81 6-87 1-81 (81)
6 PRK05435 rpmA 50S ribosomal pr 100.0 7.1E-47 1.5E-51 262.6 9.2 82 5-87 1-82 (82)
7 PF14382 ECR1_N: Exosome compl 96.0 0.014 3E-07 35.4 4.0 38 34-74 1-38 (39)
8 PRK09521 exosome complex RNA-b 95.8 0.026 5.5E-07 42.9 5.6 54 31-91 4-57 (189)
9 COG1096 Predicted RNA-binding 94.5 0.13 2.9E-06 40.8 6.3 61 30-97 3-63 (188)
10 PRK04163 exosome complex RNA-b 93.6 0.22 4.8E-06 39.4 5.9 53 29-91 5-57 (235)
11 PF03961 DUF342: Protein of un 89.7 0.97 2.1E-05 38.4 6.0 44 33-76 107-174 (451)
12 PF01551 Peptidase_M23: Peptid 88.9 1.1 2.5E-05 29.6 4.7 41 48-88 1-41 (96)
13 COG1315 Uncharacterized conser 80.1 1.9 4.1E-05 39.2 3.3 36 47-89 219-255 (543)
14 PF13533 Biotin_lipoyl_2: Biot 76.5 2.4 5.2E-05 25.9 2.1 17 27-43 16-32 (50)
15 cd06850 biotinyl_domain The bi 60.1 14 0.00031 21.9 3.1 39 27-75 13-51 (67)
16 PRK14844 bifunctional DNA-dire 59.4 20 0.00044 38.4 5.7 64 27-91 2526-2602(2836)
17 PF13375 RnfC_N: RnfC Barrel s 53.6 20 0.00044 25.3 3.4 33 29-72 46-78 (101)
18 COG1097 RRP4 RNA-binding prote 52.4 34 0.00073 28.2 4.9 54 29-91 5-58 (239)
19 PRK05889 putative acetyl-CoA c 52.4 21 0.00046 22.7 3.1 41 24-74 13-53 (71)
20 TIGR02994 ectoine_eutE ectoine 47.9 24 0.00052 29.4 3.5 42 28-76 269-311 (325)
21 PRK09603 bifunctional DNA-dire 47.1 39 0.00085 36.5 5.4 65 27-92 2616-2694(2890)
22 COG4687 Uncharacterized protei 39.2 36 0.00079 25.6 3.0 41 36-76 23-84 (122)
23 PF07370 DUF1489: Protein of u 38.9 21 0.00045 27.2 1.7 42 34-76 52-93 (137)
24 cd06253 M14_ASTE_ASPA_like_3 A 37.4 52 0.0011 26.8 3.9 41 29-76 244-284 (298)
25 PRK09774 fec operon regulator 37.3 76 0.0017 25.9 4.8 39 34-76 169-207 (319)
26 PF13540 RCC1_2: Regulator of 36.1 32 0.0007 18.9 1.8 20 55-74 4-23 (30)
27 PF00529 HlyD: HlyD family sec 35.7 24 0.00053 26.9 1.6 17 27-43 15-31 (305)
28 PRK06549 acetyl-CoA carboxylas 34.8 51 0.0011 24.4 3.2 43 21-73 69-111 (130)
29 cd06663 Biotinyl_lipoyl_domain 34.7 52 0.0011 20.4 2.8 40 25-74 17-56 (73)
30 PRK14875 acetoin dehydrogenase 33.9 45 0.00097 25.9 2.9 42 21-72 16-57 (371)
31 KOG3409 Exosomal 3'-5' exoribo 33.7 1.1E+02 0.0023 24.8 5.0 62 33-97 6-67 (193)
32 PRK08225 acetyl-CoA carboxylas 31.7 80 0.0017 19.7 3.3 42 22-73 10-51 (70)
33 COG1726 NqrA Na+-transporting 30.6 1.1E+02 0.0024 27.4 5.0 59 17-87 33-91 (447)
34 COG5455 Predicted integral mem 28.2 54 0.0012 24.9 2.4 23 45-73 101-123 (129)
35 PF02471 OspE: Borrelia outer 27.9 41 0.00089 24.8 1.6 42 30-71 13-54 (108)
36 PRK00807 50S ribosomal protein 27.6 60 0.0013 20.5 2.2 23 46-75 8-30 (52)
37 PF07883 Cupin_2: Cupin domain 27.3 1.4E+02 0.0029 17.8 3.7 12 63-74 22-33 (71)
38 PRK13918 CRP/FNR family transc 26.6 2.5E+02 0.0053 20.1 6.3 23 61-83 27-49 (202)
39 cd06251 M14_ASTE_ASPA_like_1 A 26.1 73 0.0016 25.6 2.9 40 29-76 234-273 (287)
40 PF02749 QRPTase_N: Quinolinat 26.1 46 0.00099 22.2 1.5 19 28-46 50-68 (88)
41 TIGR02971 heterocyst_DevB ABC 25.5 52 0.0011 26.1 2.0 13 61-73 205-217 (327)
42 PF07177 Neuralized: Neuralize 24.7 61 0.0013 21.3 1.9 40 47-87 2-50 (69)
43 PF00412 LIM: LIM domain; Int 22.1 71 0.0015 18.8 1.7 21 32-52 5-25 (58)
44 PF02911 Formyl_trans_C: Formy 21.9 2.3E+02 0.0051 18.3 4.6 35 51-85 57-91 (100)
45 COG0070 GltB Glutamate synthas 21.5 1.1E+02 0.0024 25.9 3.2 40 35-76 119-158 (301)
46 cd06254 M14_ASTE_ASPA_like_4 A 20.9 1.6E+02 0.0035 23.6 4.0 41 28-76 237-277 (288)
47 TIGR01015 hmgA homogentisate 1 20.7 84 0.0018 28.0 2.5 20 31-50 166-185 (429)
48 TIGR01000 bacteriocin_acc bact 20.6 69 0.0015 27.2 1.9 12 61-72 317-328 (457)
49 PLN02658 homogentisate 1,2-dio 20.1 87 0.0019 27.9 2.5 21 30-50 164-184 (435)
No 1
>COG0211 RpmA Ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3e-49 Score=276.46 Aligned_cols=86 Identities=63% Similarity=0.964 Sum_probs=83.5
Q ss_pred eeeecCCccCCCCCCCCCceeceeeeCCeEEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEEEEEecCCCceEE
Q 033652 5 WATKKTAGSTKNGRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWV 84 (114)
Q Consensus 5 ~A~KK~~GStkNgrdS~~KrLGvK~~~Gq~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~f~~~~~~~rk~V 84 (114)
|||||++|||+|||||++||||+|+++||+|.+|+||||||||+||||+|||||+|||||||+||+|+|+... ++|+||
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 7999999999999999999999999999999999999999999999999999999999999999999999986 799999
Q ss_pred EeEeCCC
Q 033652 85 HVEPKEG 91 (114)
Q Consensus 85 ~V~p~~~ 91 (114)
+|+|...
T Consensus 80 sV~~~~~ 86 (87)
T COG0211 80 SVVPEAE 86 (87)
T ss_pred EEEeecc
Confidence 9999864
No 2
>KOG4600 consensus Mitochondrial ribosomal protein MRP7 (L2) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.9e-47 Score=286.92 Aligned_cols=106 Identities=64% Similarity=1.079 Sum_probs=99.0
Q ss_pred CceEeeeecCCccCCCCCCCCCceeceeeeCCeEEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEEEEEecCC-
Q 033652 1 MFRRWATKKTAGSTKNGRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLS- 79 (114)
Q Consensus 1 ~~~r~A~KK~~GStkNgrdS~~KrLGvK~~~Gq~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~f~~~~~~- 79 (114)
+++|||+||++|||+|+|||+++|||||+|+||+|.||+||||||||+||||+|||||||||||||++|+|+|+++++.
T Consensus 24 l~vR~AtKk~aGStKN~~dS~grrlGvKk~egq~V~~G~IIvrQRgtkfHPG~nVGiGKDhtifaL~eG~Vrf~k~~~~~ 103 (144)
T KOG4600|consen 24 LAVRWATKKGAGSTKNGRDSAGRRLGVKKYEGQSVIPGNIIVRQRGTKFHPGDNVGIGKDHTIFALEEGRVRFEKSKITP 103 (144)
T ss_pred eeeeeecccccCccccCCCCCcccccceecCCeeeecccEEEEecccccCCCcccccCCcceEEEeeccEEEEEEccCCC
Confidence 3689999999999999999999999999999999999999999999999999999999999999999999999998764
Q ss_pred CceEEEeEeCCCCcccccccccccccC
Q 033652 80 GRKWVHVEPKEGHVLHPLYANATANAS 106 (114)
Q Consensus 80 ~rk~V~V~p~~~~~~~p~~~~~~~~~~ 106 (114)
.|+||+|.|...-.+||.+.++..-..
T Consensus 104 ~Rk~i~V~~~~~~~l~~~~~k~~vr~~ 130 (144)
T KOG4600|consen 104 PRKWIGVDPRGGLPLPPPYYKATVRRV 130 (144)
T ss_pred CcceEEEeecCCccCCCccchhhhhhh
Confidence 599999999999999998887766543
No 3
>CHL00121 rpl27 ribosomal protein L27; Reviewed
Probab=100.00 E-value=2.6e-47 Score=266.68 Aligned_cols=84 Identities=61% Similarity=0.907 Sum_probs=81.2
Q ss_pred eeeecCCccCCCCCCCCCceeceeeeCCeEEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEEEEEecCCCceEE
Q 033652 5 WATKKTAGSTKNGRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWV 84 (114)
Q Consensus 5 ~A~KK~~GStkNgrdS~~KrLGvK~~~Gq~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~f~~~~~~~rk~V 84 (114)
|||||++|||+|||||+|||||+|+++||+|.||+||||||||+||||+||+|||||||||+++|+|+|++.+ +++++|
T Consensus 1 mA~KK~~GStkNgrdS~~KrLGvK~~~gq~V~~G~IivRQRGtk~hPG~NVg~GrD~TlfAl~~G~V~f~~~~-~~~~~v 79 (86)
T CHL00121 1 MAHKKGAGSTKNGRDSNAKRLGVKRFGGEKVSAGNILIRQRGTKFKPGLNVGCGKDFTLYALIDGFVKFKKKN-KKQKSI 79 (86)
T ss_pred CCcccccCcCCCCCCCCcccceeEEcCCEEEcCCcEEEEcCCCeECCCCcccccCCceEEEccceEEEEEEeC-CCCEEE
Confidence 7999999999999999999999999999999999999999999999999999999999999999999999874 588899
Q ss_pred EeEeC
Q 033652 85 HVEPK 89 (114)
Q Consensus 85 ~V~p~ 89 (114)
+|+|.
T Consensus 80 sv~~~ 84 (86)
T CHL00121 80 NVINI 84 (86)
T ss_pred EEeec
Confidence 99986
No 4
>TIGR00062 L27 ribosomal protein L27. Eubacterial, chloroplast, and mitochondrial. Mitochondrial members have an additional C-terminal domain.
Probab=100.00 E-value=3.3e-47 Score=264.67 Aligned_cols=83 Identities=66% Similarity=0.990 Sum_probs=80.3
Q ss_pred eeeecCCccCCCCCCCCCceeceeeeCCeEEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEEEEEecCCCceEE
Q 033652 5 WATKKTAGSTKNGRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWV 84 (114)
Q Consensus 5 ~A~KK~~GStkNgrdS~~KrLGvK~~~Gq~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~f~~~~~~~rk~V 84 (114)
|||||++|||+|||||+|||||+|+++||+|.||+||||||||+||||+||+|||||||||+++|+|+|++.+.++|++|
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 79999999999999999999999999999999999999999999999999999999999999999999999876689999
Q ss_pred EeE
Q 033652 85 HVE 87 (114)
Q Consensus 85 ~V~ 87 (114)
+|+
T Consensus 81 ~v~ 83 (83)
T TIGR00062 81 SVV 83 (83)
T ss_pred EEC
Confidence 984
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=2.8e-47 Score=263.85 Aligned_cols=81 Identities=72% Similarity=1.122 Sum_probs=73.6
Q ss_pred eeecCCccCCCCCCCCCceeceeeeCCeEEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEEEEEecCCCceEEE
Q 033652 6 ATKKTAGSTKNGRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVH 85 (114)
Q Consensus 6 A~KK~~GStkNgrdS~~KrLGvK~~~Gq~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~f~~~~~~~rk~V~ 85 (114)
||||++|||+|||||+|||||||+++||+|.||+||||||||+||||+||+|||||||||+++|+|+|+++. ++|+||+
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 AHKKGGGSTKNGRDSNPKRLGVKKFGGQFVKAGNIIVRQRGTKFHPGENVGMGRDHTLFALVDGRVKFTKEK-RNRKYVS 79 (81)
T ss_dssp --SSSSSSSS--S-STTTTSEESSSTTCEESSTSEEEEBSSSSSEEBTTEEEETTSEEEESSSCEEEEEEET-TTEEEEE
T ss_pred CCccccccccCCCCCCCcccEEEEeCCEEEcCCCEEEEeCCCcCcCCCCEEECCCCcEEEecCEEEEEEEeC-CCCEEEE
Confidence 899999999999999999999999999999999999999999999999999999999999999999999994 6899999
Q ss_pred eE
Q 033652 86 VE 87 (114)
Q Consensus 86 V~ 87 (114)
|+
T Consensus 80 V~ 81 (81)
T PF01016_consen 80 VV 81 (81)
T ss_dssp E-
T ss_pred eC
Confidence 85
No 6
>PRK05435 rpmA 50S ribosomal protein L27; Validated
Probab=100.00 E-value=7.1e-47 Score=262.57 Aligned_cols=82 Identities=65% Similarity=0.997 Sum_probs=79.2
Q ss_pred eeeecCCccCCCCCCCCCceeceeeeCCeEEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEEEEEecCCCceEE
Q 033652 5 WATKKTAGSTKNGRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWV 84 (114)
Q Consensus 5 ~A~KK~~GStkNgrdS~~KrLGvK~~~Gq~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~f~~~~~~~rk~V 84 (114)
|||||++|||+|||||+|||||+|+++||+|.||+||||||||+||||+||+|||||||||+++|+|+|++.. ++|++|
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 7999999999999999999999999999999999999999999999999999999999999999999999874 689999
Q ss_pred EeE
Q 033652 85 HVE 87 (114)
Q Consensus 85 ~V~ 87 (114)
+|+
T Consensus 80 ~v~ 82 (82)
T PRK05435 80 SVV 82 (82)
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=96.03 E-value=0.014 Score=35.41 Aligned_cols=38 Identities=29% Similarity=0.547 Sum_probs=32.1
Q ss_pred EEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEEEE
Q 033652 34 RVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFE 74 (114)
Q Consensus 34 ~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~f~ 74 (114)
.|.||+.|... ..|.||.|+.+ +|..|||.+-|.|+..
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 47999999999 8999999999999864
No 8
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=95.82 E-value=0.026 Score=42.93 Aligned_cols=54 Identities=22% Similarity=0.395 Sum_probs=43.5
Q ss_pred CCeEEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEEEEEecCCCceEEEeEeCCC
Q 033652 31 GGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVHVEPKEG 91 (114)
Q Consensus 31 ~Gq~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~f~~~~~~~rk~V~V~p~~~ 91 (114)
+++.|.||+.|.-. -.|.||.|+.. .|.+|||.+-|.+.+..+ ++.|+|.|...
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 46999999987 678899999999999643 45577777554
No 9
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=94.53 E-value=0.13 Score=40.82 Aligned_cols=61 Identities=21% Similarity=0.338 Sum_probs=49.6
Q ss_pred eCCeEEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEEEEEecCCCceEEEeEeCCCCccccc
Q 033652 30 FGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVHVEPKEGHVLHPL 97 (114)
Q Consensus 30 ~~Gq~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~f~~~~~~~rk~V~V~p~~~~~~~p~ 97 (114)
-+|.+|.||+.|..+ -.|.||+|+--= |+.|+|...|.+..+.. .+.++|.|......+|.
T Consensus 3 ~~g~~v~PGd~~a~~--EE~~~G~gt~~~-~g~i~Aa~~G~~~~d~~----n~~~~V~p~~~~~~~~K 63 (188)
T COG1096 3 KDGTFVLPGDVLAVI--EEFLPGEGTYEE-GGEIRAAATGVVRRDDK----NRVISVKPGKKTPPLPK 63 (188)
T ss_pred ccCcEEcCcceeeee--eeeecCCCeEeE-CCEEEEeecccEEEccc----ceEEEeccCCCCCCCCC
Confidence 468899999999975 579999999876 99999999999998753 56688888776444443
No 10
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=93.60 E-value=0.22 Score=39.39 Aligned_cols=53 Identities=25% Similarity=0.396 Sum_probs=42.2
Q ss_pred eeCCeEEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEEEEEecCCCceEEEeEeCCC
Q 033652 29 KFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVHVEPKEG 91 (114)
Q Consensus 29 ~~~Gq~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~f~~~~~~~rk~V~V~p~~~ 91 (114)
..++..|.||+.|.- -.|.||.|+.. .|..|+|.+-|.+.+.. +.++|.|...
T Consensus 5 ~~~~~~V~PGd~l~~---~~~~~G~Gty~-~~g~i~As~~G~~~~~~------~~i~V~p~~~ 57 (235)
T PRK04163 5 VEDRKIVVPGDLLAE---GEFKAGRGTYK-ENGKIYSTVVGLVDIKD------DKVRVIPLEG 57 (235)
T ss_pred eeCCcEECCCCCcCc---CCeecCCceEE-eCCEEEEEEeEEEEEEC------CEEEEEECCC
Confidence 456789999999952 36999999987 78999999999999753 2577777554
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=89.75 E-value=0.97 Score=38.44 Aligned_cols=44 Identities=27% Similarity=0.514 Sum_probs=35.8
Q ss_pred eEEecCcEEEe----ccC------------------CeEeCCCCeeec-CC-CcEEEeeCeEEEEEEe
Q 033652 33 ERVIPGNIIVR----QRG------------------TRFHPGDYVGMG-KD-HTLYALKEGRVKFEKH 76 (114)
Q Consensus 33 q~V~~G~IlvR----QRG------------------tkfhPG~NVg~G-kD-~TLfAl~~G~V~f~~~ 76 (114)
..|.+|+.|++ +.| ..|.+|+||.+- .| -+|+|.++|++.|...
T Consensus 107 ~~V~~G~~la~~~p~~~G~~G~~V~G~~I~~~~~~~~~~~~g~~~~~~~~d~~~~~A~~~G~~~~~~~ 174 (451)
T PF03961_consen 107 PSVKKGDVLAEKIPPTPGEPGRDVFGEPIPAKPGKDIPLKAGKNTEVSEEDGNKLYAAIDGRPVFENG 174 (451)
T ss_pred eEECCCCEEEEEccCCCCCCCcccCCCCcCCCCCCccceeCCCCEEEEcCCCCEEEEecCCEEEEECC
Confidence 35888888887 334 578899999999 66 5799999999999954
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=88.92 E-value=1.1 Score=29.57 Aligned_cols=41 Identities=24% Similarity=0.383 Sum_probs=29.5
Q ss_pred eEeCCCCeeecCCCcEEEeeCeEEEEEEecCCCceEEEeEe
Q 033652 48 RFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVHVEP 88 (114)
Q Consensus 48 kfhPG~NVg~GkD~TLfAl~~G~V~f~~~~~~~rk~V~V~p 88 (114)
+||.|--+.......++|+.+|+|.|.......-.+|.|.-
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 58888888888778899999999999876433466666654
No 13
>COG1315 Uncharacterized conserved protein [Function unknown]
Probab=80.10 E-value=1.9 Score=39.17 Aligned_cols=36 Identities=28% Similarity=0.393 Sum_probs=29.2
Q ss_pred CeEeCCCCeeecCC-CcEEEeeCeEEEEEEecCCCceEEEeEeC
Q 033652 47 TRFHPGDYVGMGKD-HTLYALKEGRVKFEKHKLSGRKWVHVEPK 89 (114)
Q Consensus 47 tkfhPG~NVg~GkD-~TLfAl~~G~V~f~~~~~~~rk~V~V~p~ 89 (114)
..+++|.|+- -|| .||.|.++|..-+.+.. |+|+|.
T Consensus 219 ~~l~lG~nt~-~kd~~tlvA~~~G~~~~s~~t------I~V~~i 255 (543)
T COG1315 219 IKLNLGKNTA-FKDNNTLVAKRDGQPIVSKNT------ISVYPI 255 (543)
T ss_pred eeeecCCCCc-cCCCCEEEEeeCCeEEecCCe------eEEEEE
Confidence 5899999999 666 89999999999887543 677664
No 14
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=76.55 E-value=2.4 Score=25.93 Aligned_cols=17 Identities=24% Similarity=0.403 Sum_probs=15.0
Q ss_pred eeeeCCeEEecCcEEEe
Q 033652 27 VKKFGGERVIPGNIIVR 43 (114)
Q Consensus 27 vK~~~Gq~V~~G~IlvR 43 (114)
+..-.||+|++|++|++
T Consensus 16 v~V~~G~~VkkGd~L~~ 32 (50)
T PF13533_consen 16 VYVKEGQQVKKGDVLLV 32 (50)
T ss_pred EEecCCCEEcCCCEEEE
Confidence 56679999999999987
No 15
>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=60.10 E-value=14 Score=21.86 Aligned_cols=39 Identities=21% Similarity=0.129 Sum_probs=29.2
Q ss_pred eeeeCCeEEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEEEEE
Q 033652 27 VKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEK 75 (114)
Q Consensus 27 vK~~~Gq~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~f~~ 75 (114)
+..-.|++|.+|+.|++=... ..+..|.|..+|+|..-.
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 667789999999999963321 124679999999997643
No 16
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=59.37 E-value=20 Score=38.37 Aligned_cols=64 Identities=25% Similarity=0.448 Sum_probs=41.8
Q ss_pred eeeeCCeEEecCcEEEe-ccCC----eEeCCC-------CeeecCCCcEEEeeCeEEEE-EEecCCCceEEEeEeCCC
Q 033652 27 VKKFGGERVIPGNIIVR-QRGT----RFHPGD-------YVGMGKDHTLYALKEGRVKF-EKHKLSGRKWVHVEPKEG 91 (114)
Q Consensus 27 vK~~~Gq~V~~G~IlvR-QRGt----kfhPG~-------NVg~GkD~TLfAl~~G~V~f-~~~~~~~rk~V~V~p~~~ 91 (114)
+-+.+||.|.+|+||+| -|-+ -+--|. -...-++..+.|-++|+|.| .++ .+.++.|.|.+..+
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 45789999999999999 2211 011221 12355789999999999998 222 13455677777654
No 17
>PF13375 RnfC_N: RnfC Barrel sandwich hybrid domain
Probab=53.63 E-value=20 Score=25.25 Aligned_cols=33 Identities=24% Similarity=0.350 Sum_probs=24.0
Q ss_pred eeCCeEEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEE
Q 033652 29 KFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVK 72 (114)
Q Consensus 29 ~~~Gq~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~ 72 (114)
+--||+|..|++|.+-.|. + .-.|+|.++|.|.
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 4468888888888876441 1 1168999999997
No 18
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=52.40 E-value=34 Score=28.24 Aligned_cols=54 Identities=20% Similarity=0.345 Sum_probs=38.7
Q ss_pred eeCCeEEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEEEEEecCCCceEEEeEeCCC
Q 033652 29 KFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVHVEPKEG 91 (114)
Q Consensus 29 ~~~Gq~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~f~~~~~~~rk~V~V~p~~~ 91 (114)
....+.|.||++|.-+ ..|..|.++.+ +|..++|.+-|.|.++-+. +.|.|.+.
T Consensus 5 ~~~~~iV~PGd~vl~~--~~~~~G~Gty~-~~~~iyssv~G~~~~~~~~------v~VIpl~g 58 (239)
T COG1097 5 VSMRKIVLPGDLVLAE--GSYKLGHGTYF-EGGKIYSSVVGLLDVKGKL------VRVIPLEG 58 (239)
T ss_pred ccccceecCCCccCCC--CCEecCCCcEe-cCCEEEEEEEeEEEEeCCE------EEEEeCCC
Confidence 4567889999964433 23566666666 8999999999999987542 66666554
No 19
>PRK05889 putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Provisional
Probab=52.38 E-value=21 Score=22.71 Aligned_cols=41 Identities=20% Similarity=0.189 Sum_probs=29.9
Q ss_pred eeceeeeCCeEEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEEEE
Q 033652 24 NLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFE 74 (114)
Q Consensus 24 rLGvK~~~Gq~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~f~ 74 (114)
=.=+.+-.|+.|.+|+.|+-=--.| -++.|.|..+|+|.-.
T Consensus 13 i~~~~v~~Gd~V~~g~~l~~ve~~K----------~~~~I~a~~~G~V~~i 53 (71)
T PRK05889 13 VLEVVVNEGDQIGKGDTLVLLESMK----------MEIPVLAEVAGTVSKV 53 (71)
T ss_pred EEEEEeCCCCEECCCCEEEEEEecc----------ceeEEeCCCCEEEEEE
Confidence 3447788999999999998322222 3677999999998643
No 20
>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=47.86 E-value=24 Score=29.37 Aligned_cols=42 Identities=19% Similarity=0.141 Sum_probs=30.7
Q ss_pred eeeCCeEEecCcEEEeccCCeEe-CCCCeeecCCCcEEEeeCeEEEEEEe
Q 033652 28 KKFGGERVIPGNIIVRQRGTRFH-PGDYVGMGKDHTLYALKEGRVKFEKH 76 (114)
Q Consensus 28 K~~~Gq~V~~G~IlvRQRGtkfh-PG~NVg~GkD~TLfAl~~G~V~f~~~ 76 (114)
.+--|+.|.+|++|.+..- +. +|.-+ .+|.|+.+|+|-+...
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 3455899999999988764 22 34333 6899999999988654
No 21
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=47.06 E-value=39 Score=36.49 Aligned_cols=65 Identities=20% Similarity=0.295 Sum_probs=43.1
Q ss_pred eeeeCCeEEecCcEEEe-ccCCe----EeCCC-------Cee--ecCCCcEEEeeCeEEEEEEecCCCceEEEeEeCCCC
Q 033652 27 VKKFGGERVIPGNIIVR-QRGTR----FHPGD-------YVG--MGKDHTLYALKEGRVKFEKHKLSGRKWVHVEPKEGH 92 (114)
Q Consensus 27 vK~~~Gq~V~~G~IlvR-QRGtk----fhPG~-------NVg--~GkD~TLfAl~~G~V~f~~~~~~~rk~V~V~p~~~~ 92 (114)
+-+.+|+.|.+|+||+| .|-+- +--|. -.. .-+|..+.|-++|+|+|.+.. +.++.|.|.+..++
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 IAISDGSSVEQAEVLAKIPKATVKSRDITGGLPRVSELFEARKPKPKDVAILSEVDGIVSFGKPI-RNKEHIIVTSKDGR 2694 (2890)
T ss_pred EEecCCCEecccceEeeccccccccccccCCcccchhheEeecCCCCCceEEeccceEEEecccc-CCceEEEEECCCCc
Confidence 45678999999999998 44321 11111 011 346899999999999996542 34566777776643
No 22
>COG4687 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.23 E-value=36 Score=25.62 Aligned_cols=41 Identities=22% Similarity=0.519 Sum_probs=36.5
Q ss_pred ecCcEEEeccCCeEeCCCCee---------------------ecCCCcEEEeeCeEEEEEEe
Q 033652 36 IPGNIIVRQRGTRFHPGDYVG---------------------MGKDHTLYALKEGRVKFEKH 76 (114)
Q Consensus 36 ~~G~IlvRQRGtkfhPG~NVg---------------------~GkD~TLfAl~~G~V~f~~~ 76 (114)
.-|-||+=..|+.|++-.||. +|+.+.|+-...|.|.|..+
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 568999999999999988875 78899999999999999865
No 23
>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=38.91 E-value=21 Score=27.24 Aligned_cols=42 Identities=26% Similarity=0.256 Sum_probs=29.7
Q ss_pred EEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEEEEEe
Q 033652 34 RVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKH 76 (114)
Q Consensus 34 ~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~f~~~ 76 (114)
.|.+|.|++||+-+.|.|-.. +=|..++.+=+.+-.|.....
T Consensus 52 WVikg~i~~RQ~Il~i~~~~~-~dG~~rc~ivL~P~li~v~~~ 93 (137)
T PF07370_consen 52 WVIKGQIQCRQRILDIEEVTD-GDGIRRCAIVLDPELIRVEPR 93 (137)
T ss_pred EEECCEEEEeeeeeeeeEecC-CCCcccEEEEECCcEEEcccc
Confidence 599999999999988877432 113346777777777776543
No 24
>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=37.41 E-value=52 Score=26.79 Aligned_cols=41 Identities=20% Similarity=0.216 Sum_probs=28.5
Q ss_pred eeCCeEEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEEEEEe
Q 033652 29 KFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKH 76 (114)
Q Consensus 29 ~~~Gq~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~f~~~ 76 (114)
+--|+.|.+|++|.+..-. ++|+-+ .++.|+.+|.|-+...
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 4799999999998764
No 25
>PRK09774 fec operon regulator FecR; Reviewed
Probab=37.26 E-value=76 Score=25.85 Aligned_cols=39 Identities=23% Similarity=0.227 Sum_probs=33.3
Q ss_pred EEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEEEEEe
Q 033652 34 RVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKH 76 (114)
Q Consensus 34 ~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~f~~~ 76 (114)
.|.+|+.-|+-.||+| ||-.-.+.+-.++.+|.|++...
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 4667888899999998 68888888999999999999764
No 26
>PF13540 RCC1_2: Regulator of chromosome condensation (RCC1) repeat; PDB: 3QI0_D 1JTD_B 3QHY_B.
Probab=36.07 E-value=32 Score=18.87 Aligned_cols=20 Identities=25% Similarity=0.230 Sum_probs=16.0
Q ss_pred eeecCCCcEEEeeCeEEEEE
Q 033652 55 VGMGKDHTLYALKEGRVKFE 74 (114)
Q Consensus 55 Vg~GkD~TLfAl~~G~V~f~ 74 (114)
|-.|.+||+.=+.+|.|.--
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 67899999999999998643
No 27
>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=35.73 E-value=24 Score=26.90 Aligned_cols=17 Identities=29% Similarity=0.528 Sum_probs=10.5
Q ss_pred eeeeCCeEEecCcEEEe
Q 033652 27 VKKFGGERVIPGNIIVR 43 (114)
Q Consensus 27 vK~~~Gq~V~~G~IlvR 43 (114)
|-+-+||+|.+|++|++
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 34567888888888876
No 28
>PRK06549 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=34.82 E-value=51 Score=24.41 Aligned_cols=43 Identities=16% Similarity=0.175 Sum_probs=33.5
Q ss_pred CCceeceeeeCCeEEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEEE
Q 033652 21 KPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKF 73 (114)
Q Consensus 21 ~~KrLGvK~~~Gq~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~f 73 (114)
.++=+=|....|+.|.+|+.|+.=.-+|. ...|.|..+|+|..
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 35556688999999999999997554442 46799999999964
No 29
>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=34.74 E-value=52 Score=20.39 Aligned_cols=40 Identities=23% Similarity=0.263 Sum_probs=28.0
Q ss_pred eceeeeCCeEEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEEEE
Q 033652 25 LGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFE 74 (114)
Q Consensus 25 LGvK~~~Gq~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~f~ 74 (114)
+=+.+-.|+.|.+|+.|..=-..+ -...|.|+.+|.|.-.
T Consensus 17 ~~~~v~~G~~v~~g~~l~~ie~~k----------~~~~i~ap~~G~v~~~ 56 (73)
T cd06663 17 VKWLKKVGDKVKKGDVLAEIEAMK----------ATSDVEAPKSGTVKKV 56 (73)
T ss_pred EEEEcCCcCEECCCCEEEEEEeCC----------eEEEEEcCCCEEEEEE
Confidence 336667899999998888732221 1456899999998744
No 30
>PRK14875 acetoin dehydrogenase E2 subunit dihydrolipoyllysine-residue acetyltransferase; Provisional
Probab=33.93 E-value=45 Score=25.89 Aligned_cols=42 Identities=17% Similarity=0.151 Sum_probs=31.7
Q ss_pred CCceeceeeeCCeEEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEE
Q 033652 21 KPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVK 72 (114)
Q Consensus 21 ~~KrLGvK~~~Gq~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~ 72 (114)
.++=.-|.+-.|+.|.+|++|+.--. |--.+.+-|+.+|+|.
T Consensus 16 ~g~~~~~~~~~g~~v~~~~~~~~~e~----------~k~~~~~~a~~~g~~~ 57 (371)
T PRK14875 16 EGKVAGWLVQEGDEVEKGDELLDVET----------DKITNEVEAPAAGTLR 57 (371)
T ss_pred eEEEEEEEcCCCCEeCCCCEEEEEEe----------cceeEEEecCCCeEEE
Confidence 45556678889999999999998222 2234778999999987
No 31
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=33.68 E-value=1.1e+02 Score=24.77 Aligned_cols=62 Identities=21% Similarity=0.283 Sum_probs=39.1
Q ss_pred eEEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEEEEEecCCCceEEEeEeCCCCccccc
Q 033652 33 ERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVHVEPKEGHVLHPL 97 (114)
Q Consensus 33 q~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~f~~~~~~~rk~V~V~p~~~~~~~p~ 97 (114)
-+|.||+.+.|--+- +.+|++..-- +..|||...|.+.++.. ..+...+++.......+.|.
T Consensus 6 ~~~lpG~~~c~~e~~-~~~g~Gtye~-~~yI~aS~ag~~~~~~~-~~~~~v~~~~~~~~~~~LP~ 67 (193)
T KOG3409|consen 6 TLVLPGEVVCRAEGE-YRMGEGTYER-NGYIFASVAGVNFRDNL-VQKIEVVSVEKQLFNELLPF 67 (193)
T ss_pred EEEcccceeeecccc-cccccceeec-CCeEEeccccceeecCC-ccceeeeeecccchhhcCCc
Confidence 367888888886652 3677766543 34899999996655522 24556666655554555553
No 32
>PRK08225 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=31.67 E-value=80 Score=19.75 Aligned_cols=42 Identities=19% Similarity=0.144 Sum_probs=29.7
Q ss_pred CceeceeeeCCeEEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEEE
Q 033652 22 PKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKF 73 (114)
Q Consensus 22 ~KrLGvK~~~Gq~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~f 73 (114)
++-.-+..-.|+.|.+|+.|..=.-.| -...+.|..+|+|.-
T Consensus 10 G~i~~~~v~~G~~V~~g~~l~~ve~~k----------~~~~v~s~~~G~v~~ 51 (70)
T PRK08225 10 GNVWKIVVKVGDTVEEGQDVVILESMK----------MEIPIVAEEAGTVKK 51 (70)
T ss_pred EEEEEEEeCCCCEECCCCEEEEEEcCC----------CcceEeCCCCEEEEE
Confidence 333446777799999999998733322 266799999998853
No 33
>COG1726 NqrA Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrA [Energy production and conversion]
Probab=30.56 E-value=1.1e+02 Score=27.45 Aligned_cols=59 Identities=22% Similarity=0.269 Sum_probs=43.3
Q ss_pred CCCCCCceeceeeeCCeEEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEEEEEecCCCceEEEeE
Q 033652 17 GRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVHVE 87 (114)
Q Consensus 17 grdS~~KrLGvK~~~Gq~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~f~~~~~~~rk~V~V~ 87 (114)
|++=.|-|+++|+..|+.|.+|++|.--. -.|| |. +-|+++|.|.=-..+ .+|..-+|+
T Consensus 33 g~ey~gmrp~mkV~~gD~VkkGq~LfEdK---knpg--v~------~Tap~sG~V~aI~RG-~KRvLqsVV 91 (447)
T COG1726 33 GEEYVGMRPSMKVREGDAVKKGQVLFEDK---KNPG--VV------FTAPVSGKVTAIHRG-EKRVLQSVV 91 (447)
T ss_pred cccccCCCCcceeccCCeeeccceeeecc---cCCC--eE------EeccCCceEEEeecc-cceeeeeEE
Confidence 55667889999999999999999998643 3444 32 459999999865554 466665553
No 34
>COG5455 Predicted integral membrane protein [Function unknown]
Probab=28.21 E-value=54 Score=24.91 Aligned_cols=23 Identities=35% Similarity=0.598 Sum_probs=18.5
Q ss_pred cCCeEeCCCCeeecCCCcEEEeeCeEEEE
Q 033652 45 RGTRFHPGDYVGMGKDHTLYALKEGRVKF 73 (114)
Q Consensus 45 RGtkfhPG~NVg~GkD~TLfAl~~G~V~f 73 (114)
||+.| |.||-||-|.+..+| |-|
T Consensus 101 RGq~W-----vrvg~dyvLi~~~tG-lI~ 123 (129)
T COG5455 101 RGQHW-----VRVGGDYVLISDTTG-LIF 123 (129)
T ss_pred CCcee-----EEECCeEEEEeecCc-eEE
Confidence 45555 899999999999999 444
No 35
>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=27.94 E-value=41 Score=24.78 Aligned_cols=42 Identities=29% Similarity=0.462 Sum_probs=34.0
Q ss_pred eCCeEEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEE
Q 033652 30 FGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRV 71 (114)
Q Consensus 30 ~~Gq~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V 71 (114)
..+...--|..+||.-.--+--|.||+.|..-|+|++.+--|
T Consensus 13 n~~nW~dLGtLvv~KeedgI~tgLN~~~GhsatfFsleesEv 54 (108)
T PF02471_consen 13 NSGNWTDLGTLVVRKEEDGIETGLNVGGGHSATFFSLEESEV 54 (108)
T ss_pred CCCCceeeeeEEEEeecCceeeccccCCCceEEEEEecHHHH
Confidence 455667778889998888899999999999999999876433
No 36
>PRK00807 50S ribosomal protein L24e; Validated
Probab=27.65 E-value=60 Score=20.49 Aligned_cols=23 Identities=26% Similarity=0.541 Sum_probs=16.2
Q ss_pred CCeEeCCCCeeecCCCcEEEeeCeEEEEEE
Q 033652 46 GTRFHPGDYVGMGKDHTLYALKEGRVKFEK 75 (114)
Q Consensus 46 GtkfhPG~NVg~GkD~TLfAl~~G~V~f~~ 75 (114)
|.+++||.+. +|...||.|.+-.
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 7889999874 4566777776654
No 37
>PF07883 Cupin_2: Cupin domain; InterPro: IPR013096 This family represents the conserved barrel domain of the cupin superfamily [] (cupa is the Latin term for a small barrel). ; PDB: 2OPK_C 3BU7_B 2PHD_D 3NVC_A 3NKT_A 3NJZ_A 3NW4_A 3NST_A 3NL1_A 2H0V_A ....
Probab=27.27 E-value=1.4e+02 Score=17.77 Aligned_cols=12 Identities=8% Similarity=0.293 Sum_probs=5.7
Q ss_pred EEEeeCeEEEEE
Q 033652 63 LYALKEGRVKFE 74 (114)
Q Consensus 63 LfAl~~G~V~f~ 74 (114)
++=..+|.+.+.
T Consensus 22 ~~~vl~G~~~~~ 33 (71)
T PF07883_consen 22 FFYVLSGEGTLT 33 (71)
T ss_dssp EEEEEESEEEEE
T ss_pred EEEEEECCEEEE
Confidence 444445555544
No 38
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=26.57 E-value=2.5e+02 Score=20.15 Aligned_cols=23 Identities=22% Similarity=0.424 Sum_probs=17.3
Q ss_pred CcEEEeeCeEEEEEEecCCCceE
Q 033652 61 HTLYALKEGRVKFEKHKLSGRKW 83 (114)
Q Consensus 61 ~TLfAl~~G~V~f~~~~~~~rk~ 83 (114)
..+|-+.+|.|+.+......+..
T Consensus 27 ~~~y~I~~G~vr~~~~~~~G~e~ 49 (202)
T PRK13918 27 DMLYRVRSGLVRLHTVDDEGNAL 49 (202)
T ss_pred CeEEEEEeeEEEEEEECCCCCEE
Confidence 67999999999998764444433
No 39
>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=26.11 E-value=73 Score=25.58 Aligned_cols=40 Identities=18% Similarity=0.178 Sum_probs=26.7
Q ss_pred eeCCeEEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEEEEEe
Q 033652 29 KFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKH 76 (114)
Q Consensus 29 ~~~Gq~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~f~~~ 76 (114)
+--|+.|.+|+.|.+..-. -| ..-.++.|+.+|.|.+...
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 4457788888888775431 11 1126899999999976553
No 40
>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=26.06 E-value=46 Score=22.25 Aligned_cols=19 Identities=37% Similarity=0.676 Sum_probs=14.5
Q ss_pred eeeCCeEEecCcEEEeccC
Q 033652 28 KKFGGERVIPGNIIVRQRG 46 (114)
Q Consensus 28 K~~~Gq~V~~G~IlvRQRG 46 (114)
.+.||+.|.+|++|++=+|
T Consensus 50 ~~~dG~~v~~g~~i~~i~G 68 (88)
T PF02749_consen 50 LVKDGDRVEPGDVILEIEG 68 (88)
T ss_dssp SS-TT-EEETTCEEEEEEE
T ss_pred EeCCCCCccCCcEEEEEEe
Confidence 3479999999999998766
No 41
>TIGR02971 heterocyst_DevB ABC exporter membrane fusion protein, DevB family. Members of this protein family are found mostly in the Cyanobacteria, but also in the Planctomycetes. DevB from Anabaena sp. strain PCC 7120 is partially characterized as a membrane fusion protein of the DevBCA ABC exporter, probably a glycolipid exporter, required for heterocyst formation. Most Cyanobacteria have one member only, but Nostoc sp. PCC 7120 has seven members.
Probab=25.51 E-value=52 Score=26.07 Aligned_cols=13 Identities=31% Similarity=0.194 Sum_probs=8.9
Q ss_pred CcEEEeeCeEEEE
Q 033652 61 HTLYALKEGRVKF 73 (114)
Q Consensus 61 ~TLfAl~~G~V~f 73 (114)
.+|.|+++|+|.-
T Consensus 205 ~~i~AP~dG~V~~ 217 (327)
T TIGR02971 205 TYVKAPIDGRVLK 217 (327)
T ss_pred CEEECCCCeEEEE
Confidence 4677777777753
No 42
>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=24.74 E-value=61 Score=21.30 Aligned_cols=40 Identities=30% Similarity=0.500 Sum_probs=20.3
Q ss_pred CeEeC---CCCeeecCCCcEEEe----eCeEEEEEEecCCC--ceEEEeE
Q 033652 47 TRFHP---GDYVGMGKDHTLYAL----KEGRVKFEKHKLSG--RKWVHVE 87 (114)
Q Consensus 47 tkfhP---G~NVg~GkD~TLfAl----~~G~V~f~~~~~~~--rk~V~V~ 87 (114)
+.||| |.||-|..|.+.-.- .+| +.|+..+... ...|.|.
T Consensus 2 l~FH~~~~G~nV~L~~~~~~A~R~~sf~~g-iVFS~rPl~~~E~~~v~I~ 50 (69)
T PF07177_consen 2 LRFHPNVHGKNVRLSNDGTVARRVSSFNNG-IVFSSRPLRIGEKFEVRID 50 (69)
T ss_dssp --EEC-EE-TTEEE-SSS-EEEEST-SSS--EEEESS-B-TT-EEEEEEE
T ss_pred ccccCcccCCCEEEcCCCeEEEecccCCce-EEEecCCccCCCEEEEEEE
Confidence 46998 999999999975332 234 5577665443 3344443
No 43
>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=22.07 E-value=71 Score=18.80 Aligned_cols=21 Identities=24% Similarity=0.610 Sum_probs=17.1
Q ss_pred CeEEecCcEEEeccCCeEeCC
Q 033652 32 GERVIPGNIIVRQRGTRFHPG 52 (114)
Q Consensus 32 Gq~V~~G~IlvRQRGtkfhPG 52 (114)
++.|.++.++++..|..|||-
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 44
>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=21.92 E-value=2.3e+02 Score=18.28 Aligned_cols=35 Identities=26% Similarity=0.412 Sum_probs=25.6
Q ss_pred CCCCeeecCCCcEEEeeCeEEEEEEecCCCceEEE
Q 033652 51 PGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVH 85 (114)
Q Consensus 51 PG~NVg~GkD~TLfAl~~G~V~f~~~~~~~rk~V~ 85 (114)
||.=+.+.++.=+++..+|.|.+..-....++.++
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 88877888887788999999998765444555443
No 45
>COG0070 GltB Glutamate synthase domain 3 [Amino acid transport and metabolism]
Probab=21.53 E-value=1.1e+02 Score=25.93 Aligned_cols=40 Identities=25% Similarity=0.465 Sum_probs=33.3
Q ss_pred EecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEEEEEe
Q 033652 35 VIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKH 76 (114)
Q Consensus 35 V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~f~~~ 76 (114)
..-|.|+||-. ..|.|.+|+-+| |.+||....|.+.+.-.
T Consensus 119 msgG~IVV~~~-~~~~~~~~~i~G-n~~lyGatgG~~fi~G~ 158 (301)
T COG0070 119 MSGGKIVVRGP-ARFKAEANIIVG-NTVLYGATGGELFIRGN 158 (301)
T ss_pred CCCcEEEEECC-CcccccCCceec-ceEEEeccCcEEEEecC
Confidence 45678888877 699999997776 89999999999998653
No 46
>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=20.91 E-value=1.6e+02 Score=23.56 Aligned_cols=41 Identities=17% Similarity=0.113 Sum_probs=28.6
Q ss_pred eeeCCeEEecCcEEEeccCCeEeCCCCeeecCCCcEEEeeCeEEEEEEe
Q 033652 28 KKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKH 76 (114)
Q Consensus 28 K~~~Gq~V~~G~IlvRQRGtkfhPG~NVg~GkD~TLfAl~~G~V~f~~~ 76 (114)
++.-|+.|.+|++|....-.- |+ ..+++.|+.+|.|-+...
T Consensus 237 ~~~~G~~V~~G~~lg~i~dp~---g~-----~~~~i~Ap~dG~v~~~~~ 277 (288)
T cd06254 237 FVKAGDTVQKGALLGYVTDYF---GN-----VIAEYRAPFDGVVLYNTA 277 (288)
T ss_pred ecCCCCEecCCCEEEEEECCC---CC-----ceEEEEcCCCcEEEEeeC
Confidence 344688888888887765421 21 136799999999988754
No 47
>TIGR01015 hmgA homogentisate 1,2-dioxygenase. Missing in human disease alkaptonuria.
Probab=20.75 E-value=84 Score=28.00 Aligned_cols=20 Identities=45% Similarity=0.625 Sum_probs=16.3
Q ss_pred CCeEEecCcEEEeccCCeEe
Q 033652 31 GGERVIPGNIIVRQRGTRFH 50 (114)
Q Consensus 31 ~Gq~V~~G~IlvRQRGtkfh 50 (114)
+--.|.+|+|+|=|||++|.
T Consensus 166 G~L~v~pgei~VIPRG~~fr 185 (429)
T TIGR01015 166 GRLLVEPNEICVIPRGVRFR 185 (429)
T ss_pred cceEecCCCEEEecCccEEE
Confidence 34478999999999999764
No 48
>TIGR01000 bacteriocin_acc bacteriocin secretion accessory protein. This family represents an accessory protein that works with the bacteriocin maturation and ABC transport secretion protein described by TIGR01193.
Probab=20.60 E-value=69 Score=27.22 Aligned_cols=12 Identities=17% Similarity=0.288 Sum_probs=7.1
Q ss_pred CcEEEeeCeEEE
Q 033652 61 HTLYALKEGRVK 72 (114)
Q Consensus 61 ~TLfAl~~G~V~ 72 (114)
.+|.|+.||+|.
T Consensus 317 ~~I~AP~dG~V~ 328 (457)
T TIGR01000 317 GVIKAPEDGVLH 328 (457)
T ss_pred CEEECCCCeEEE
Confidence 456666666665
No 49
>PLN02658 homogentisate 1,2-dioxygenase
Probab=20.12 E-value=87 Score=27.94 Aligned_cols=21 Identities=48% Similarity=0.806 Sum_probs=16.0
Q ss_pred eCCeEEecCcEEEeccCCeEe
Q 033652 30 FGGERVIPGNIIVRQRGTRFH 50 (114)
Q Consensus 30 ~~Gq~V~~G~IlvRQRGtkfh 50 (114)
++--.|.+|+|+|=|||++|.
T Consensus 164 fG~L~v~pgei~VIPRG~~fr 184 (435)
T PLN02658 164 LGKLQVSPGEIVVIPRGFRFA 184 (435)
T ss_pred ccceEecCCCEEEecCccEEE
Confidence 334467899999999998775
Done!