Query 032857
Match_columns 132
No_of_seqs 116 out of 1033
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 06:47:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032857.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032857hhsearch_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 1.6E-47 3.6E-52 293.7 10.0 112 10-121 15-127 (144)
2 COG0211 RpmA Ribosomal protein 100.0 2.4E-47 5.3E-52 272.7 8.8 86 23-109 1-86 (87)
3 CHL00121 rpl27 ribosomal prote 100.0 9.7E-46 2.1E-50 264.5 9.3 84 23-107 1-84 (86)
4 PF01016 Ribosomal_L27: Riboso 100.0 6.6E-46 1.4E-50 262.8 7.7 81 24-105 1-81 (81)
5 TIGR00062 L27 ribosomal protei 100.0 1.4E-45 2.9E-50 262.3 9.0 83 23-105 1-83 (83)
6 PRK05435 rpmA 50S ribosomal pr 100.0 2.8E-45 6E-50 260.3 9.4 82 23-105 1-82 (82)
7 PF14382 ECR1_N: Exosome compl 95.7 0.022 4.7E-07 35.4 4.1 38 52-92 1-38 (39)
8 PRK09521 exosome complex RNA-b 95.6 0.033 7.2E-07 43.4 5.6 54 49-109 4-57 (189)
9 COG1096 Predicted RNA-binding 94.6 0.13 2.7E-06 42.0 6.4 61 48-115 3-63 (188)
10 PRK04163 exosome complex RNA-b 93.4 0.24 5.3E-06 40.2 6.0 54 47-110 5-58 (235)
11 PF01551 Peptidase_M23: Peptid 89.3 1.1 2.5E-05 30.3 5.0 42 66-107 1-42 (96)
12 PF03961 DUF342: Protein of un 87.9 1.5 3.2E-05 38.3 6.0 44 51-94 107-174 (451)
13 COG1315 Uncharacterized conser 76.8 2.7 5.8E-05 39.1 3.4 36 65-107 219-255 (543)
14 PF13533 Biotin_lipoyl_2: Biot 71.2 3.8 8.2E-05 25.7 2.1 18 44-61 15-32 (50)
15 PRK14844 bifunctional DNA-dire 59.6 19 0.00042 39.5 5.7 64 45-109 2526-2602(2836)
16 cd06850 biotinyl_domain The bi 55.7 27 0.00058 21.2 3.9 39 45-93 13-51 (67)
17 COG1097 RRP4 RNA-binding prote 50.2 39 0.00085 28.5 5.1 54 47-109 5-58 (239)
18 PF13375 RnfC_N: RnfC Barrel s 47.6 27 0.00059 25.2 3.4 33 47-90 46-78 (101)
19 TIGR02994 ectoine_eutE ectoine 46.3 28 0.0006 29.7 3.7 42 46-94 269-311 (325)
20 PRK05889 putative acetyl-CoA c 44.5 34 0.00074 22.3 3.2 40 43-92 14-53 (71)
21 PRK09603 bifunctional DNA-dire 42.3 69 0.0015 35.6 6.5 65 45-110 2616-2694(2890)
22 cd06253 M14_ASTE_ASPA_like_3 A 33.4 66 0.0014 26.9 4.0 41 47-94 244-284 (298)
23 KOG3409 Exosomal 3'-5' exoribo 33.3 1.1E+02 0.0023 25.4 5.0 62 52-116 7-68 (193)
24 PRK09774 fec operon regulator 32.8 88 0.0019 26.2 4.6 39 52-94 169-207 (319)
25 COG4687 Uncharacterized protei 32.7 56 0.0012 25.2 3.1 41 54-94 23-84 (122)
26 PF07177 Neuralized: Neuralize 32.2 84 0.0018 21.2 3.7 38 65-103 2-46 (69)
27 PF07370 DUF1489: Protein of u 31.4 33 0.00071 26.8 1.7 41 52-93 52-92 (137)
28 PF13540 RCC1_2: Regulator of 31.3 54 0.0012 18.4 2.2 20 73-92 4-23 (30)
29 cd06663 Biotinyl_lipoyl_domain 30.1 75 0.0016 20.2 3.1 39 45-93 19-57 (73)
30 PRK13918 CRP/FNR family transc 29.6 2.3E+02 0.005 20.8 6.3 23 79-101 27-49 (202)
31 PRK06549 acetyl-CoA carboxylas 29.4 74 0.0016 24.1 3.3 43 39-91 69-111 (130)
32 PF07883 Cupin_2: Cupin domain 29.4 1.4E+02 0.003 18.2 4.4 12 81-92 22-33 (71)
33 COG1726 NqrA Na+-transporting 28.4 1.3E+02 0.0027 27.7 5.1 58 35-104 33-90 (447)
34 PF00529 HlyD: HlyD family sec 27.7 39 0.00085 26.4 1.6 17 45-61 15-31 (305)
35 PF02471 OspE: Borrelia outer 26.4 48 0.001 25.0 1.8 41 49-89 14-54 (108)
36 PRK14875 acetoin dehydrogenase 26.3 78 0.0017 25.2 3.1 42 39-90 16-57 (371)
37 PRK08225 acetyl-CoA carboxylas 25.5 1.1E+02 0.0024 19.6 3.3 39 43-91 13-51 (70)
38 PRK00807 50S ribosomal protein 25.3 67 0.0015 20.8 2.1 23 64-93 8-30 (52)
39 PRK11637 AmiB activator; Provi 25.0 1.1E+02 0.0024 26.5 4.1 47 47-94 302-355 (428)
40 PF02749 QRPTase_N: Quinolinat 23.1 56 0.0012 22.4 1.6 20 45-64 49-68 (88)
41 PF07290 DUF1449: Protein of u 22.9 1.6E+02 0.0034 24.0 4.3 27 85-112 152-178 (202)
42 COG5455 Predicted integral mem 22.4 87 0.0019 24.4 2.6 18 73-91 106-123 (129)
43 cd06251 M14_ASTE_ASPA_like_1 A 21.9 1.1E+02 0.0024 25.2 3.3 40 47-94 234-273 (287)
44 PF00412 LIM: LIM domain; Int 20.7 81 0.0017 19.0 1.8 21 50-70 5-25 (58)
45 TIGR02971 heterocyst_DevB ABC 20.3 74 0.0016 25.9 2.0 19 43-61 28-46 (327)
No 1
>KOG4600 consensus Mitochondrial ribosomal protein MRP7 (L2) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.6e-47 Score=293.68 Aligned_cols=112 Identities=66% Similarity=1.114 Sum_probs=104.3
Q ss_pred cCCCCCcceeeeeeeeccCCccCCCCCCCCCccceeeeeCCeEEecCcEEeecccceEeCCCceeecCCccEEEeeCeEE
Q 032857 10 DGSAGGLSLMFRRWATKKTAGSTKNGRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRV 89 (132)
Q Consensus 10 ~~~~~~~~~~~~r~A~KK~~GStkNGrdS~~KrLGiK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V 89 (132)
...+++++.+++|||+||++|||+|+|||+|+|||||+|+||+|.||+||||||||+||||+|||||||||||||++|+|
T Consensus 15 ~~~ss~~~~l~vR~AtKk~aGStKN~~dS~grrlGvKk~egq~V~~G~IIvrQRgtkfHPG~nVGiGKDhtifaL~eG~V 94 (144)
T KOG4600|consen 15 DGSSSGLSFLAVRWATKKGAGSTKNGRDSAGRRLGVKKYEGQSVIPGNIIVRQRGTKFHPGDNVGIGKDHTIFALEEGRV 94 (144)
T ss_pred cCCCCcceeeeeeeecccccCccccCCCCCcccccceecCCeeeecccEEEEecccccCCCcccccCCcceEEEeeccEE
Confidence 45566778999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEecCCC-ceEEEeeeCCCCccccccccccc
Q 032857 90 KFEKHKLSG-RKWVHVEPKEGHVLHPLYANATA 121 (132)
Q Consensus 90 ~f~~~~~~~-r~~V~V~p~~~~~~hp~~~~~~~ 121 (132)
+|+++++.. |+||+|+|-....+||.+.++..
T Consensus 95 rf~k~~~~~~Rk~i~V~~~~~~~l~~~~~k~~v 127 (144)
T KOG4600|consen 95 RFEKSKITPPRKWIGVDPRGGLPLPPPYYKATV 127 (144)
T ss_pred EEEEccCCCCcceEEEeecCCccCCCccchhhh
Confidence 999987654 99999999999999998876654
No 2
>COG0211 RpmA Ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.4e-47 Score=272.67 Aligned_cols=86 Identities=63% Similarity=0.964 Sum_probs=83.4
Q ss_pred eeeccCCccCCCCCCCCCccceeeeeCCeEEecCcEEeecccceEeCCCceeecCCccEEEeeCeEEEEEEecCCCceEE
Q 032857 23 WATKKTAGSTKNGRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWV 102 (132)
Q Consensus 23 ~A~KK~~GStkNGrdS~~KrLGiK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V~f~~~~~~~r~~V 102 (132)
|||||++|||+|||||++||||+|+|+||+|.+|+||||||||+||||+|||||+|||||||++|+|+|+... ++|+||
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 032857 103 HVEPKEG 109 (132)
Q Consensus 103 ~V~p~~~ 109 (132)
+|+|...
T Consensus 80 sV~~~~~ 86 (87)
T COG0211 80 SVVPEAE 86 (87)
T ss_pred EEEeecc
Confidence 9999764
No 3
>CHL00121 rpl27 ribosomal protein L27; Reviewed
Probab=100.00 E-value=9.7e-46 Score=264.50 Aligned_cols=84 Identities=61% Similarity=0.907 Sum_probs=81.1
Q ss_pred eeeccCCccCCCCCCCCCccceeeeeCCeEEecCcEEeecccceEeCCCceeecCCccEEEeeCeEEEEEEecCCCceEE
Q 032857 23 WATKKTAGSTKNGRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWV 102 (132)
Q Consensus 23 ~A~KK~~GStkNGrdS~~KrLGiK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V~f~~~~~~~r~~V 102 (132)
|||||++|||+|||||+|||||+|+++||+|.||+||||||||+||||+||+|||||||||+++|+|+|++.. +++++|
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 688999
Q ss_pred EeeeC
Q 032857 103 HVEPK 107 (132)
Q Consensus 103 ~V~p~ 107 (132)
+|+|.
T Consensus 80 sv~~~ 84 (86)
T CHL00121 80 NVINI 84 (86)
T ss_pred EEeec
Confidence 99986
No 4
>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=6.6e-46 Score=262.78 Aligned_cols=81 Identities=72% Similarity=1.122 Sum_probs=73.6
Q ss_pred eeccCCccCCCCCCCCCccceeeeeCCeEEecCcEEeecccceEeCCCceeecCCccEEEeeCeEEEEEEecCCCceEEE
Q 032857 24 ATKKTAGSTKNGRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVH 103 (132)
Q Consensus 24 A~KK~~GStkNGrdS~~KrLGiK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V~f~~~~~~~r~~V~ 103 (132)
||||++|||+|||||+|||||||+++||+|.||+||||||||+||||+||+|||||||||+++|+|+|+++. ++|+||+
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 7899999
Q ss_pred ee
Q 032857 104 VE 105 (132)
Q Consensus 104 V~ 105 (132)
|+
T Consensus 80 V~ 81 (81)
T PF01016_consen 80 VV 81 (81)
T ss_dssp E-
T ss_pred eC
Confidence 85
No 5
>TIGR00062 L27 ribosomal protein L27. Eubacterial, chloroplast, and mitochondrial. Mitochondrial members have an additional C-terminal domain.
Probab=100.00 E-value=1.4e-45 Score=262.32 Aligned_cols=83 Identities=66% Similarity=0.990 Sum_probs=80.3
Q ss_pred eeeccCCccCCCCCCCCCccceeeeeCCeEEecCcEEeecccceEeCCCceeecCCccEEEeeCeEEEEEEecCCCceEE
Q 032857 23 WATKKTAGSTKNGRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWV 102 (132)
Q Consensus 23 ~A~KK~~GStkNGrdS~~KrLGiK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V~f~~~~~~~r~~V 102 (132)
|||||++|||+|||||+|||||||+++||+|.||+||||||||+||||+||+|||||||||+++|+|+|++++.++|+||
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 79999999999999999999999999999999999999999999999999999999999999999999999865689999
Q ss_pred Eee
Q 032857 103 HVE 105 (132)
Q Consensus 103 ~V~ 105 (132)
+|+
T Consensus 81 ~v~ 83 (83)
T TIGR00062 81 SVV 83 (83)
T ss_pred EEC
Confidence 984
No 6
>PRK05435 rpmA 50S ribosomal protein L27; Validated
Probab=100.00 E-value=2.8e-45 Score=260.26 Aligned_cols=82 Identities=65% Similarity=0.997 Sum_probs=79.2
Q ss_pred eeeccCCccCCCCCCCCCccceeeeeCCeEEecCcEEeecccceEeCCCceeecCCccEEEeeCeEEEEEEecCCCceEE
Q 032857 23 WATKKTAGSTKNGRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWV 102 (132)
Q Consensus 23 ~A~KK~~GStkNGrdS~~KrLGiK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V~f~~~~~~~r~~V 102 (132)
|||||++|||+|||||+|||||||+++||+|.||+||||||||+||||+||+|||||||||+++|+|+|++.. ++|+||
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 032857 103 HVE 105 (132)
Q Consensus 103 ~V~ 105 (132)
+|+
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=95.74 E-value=0.022 Score=35.35 Aligned_cols=38 Identities=29% Similarity=0.547 Sum_probs=32.0
Q ss_pred EEecCcEEeecccceEeCCCceeecCCccEEEeeCeEEEEE
Q 032857 52 RVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFE 92 (132)
Q Consensus 52 ~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V~f~ 92 (132)
.|.||+.|-.. ..|.||.|+.+ +|..|||.+-|.|+..
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=95.60 E-value=0.033 Score=43.40 Aligned_cols=54 Identities=22% Similarity=0.395 Sum_probs=43.8
Q ss_pred CCeEEecCcEEeecccceEeCCCceeecCCccEEEeeCeEEEEEEecCCCceEEEeeeCCC
Q 032857 49 GGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVHVEPKEG 109 (132)
Q Consensus 49 ~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V~f~~~~~~~r~~V~V~p~~~ 109 (132)
+++.|.||+.|.-. -.|.||.|+.. +|.+|||.+-|.+.+..+ ++.|+|.|...
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 678899999999999543 45578877654
No 9
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=94.57 E-value=0.13 Score=41.97 Aligned_cols=61 Identities=21% Similarity=0.329 Sum_probs=50.6
Q ss_pred eCCeEEecCcEEeecccceEeCCCceeecCCccEEEeeCeEEEEEEecCCCceEEEeeeCCCCccccc
Q 032857 48 FGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVHVEPKEGHVLHPL 115 (132)
Q Consensus 48 ~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V~f~~~~~~~r~~V~V~p~~~~~~hp~ 115 (132)
..|.+|.||+.|..+ -.|.||+|+--= |+.|+|...|.+..+. +.+.++|.|......+|.
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-GGEIRAAATGVVRRDD----KNRVISVKPGKKTPPLPK 63 (188)
T ss_pred ccCcEEcCcceeeee--eeeecCCCeEeE-CCEEEEeecccEEEcc----cceEEEeccCCCCCCCCC
Confidence 468899999999975 579999999876 9999999999998875 366789999887555554
No 10
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=93.41 E-value=0.24 Score=40.16 Aligned_cols=54 Identities=24% Similarity=0.392 Sum_probs=43.0
Q ss_pred eeCCeEEecCcEEeecccceEeCCCceeecCCccEEEeeCeEEEEEEecCCCceEEEeeeCCCC
Q 032857 47 KFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVHVEPKEGH 110 (132)
Q Consensus 47 ~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V~f~~~~~~~r~~V~V~p~~~~ 110 (132)
..++..|.||+.|.- -.|.||.|+.. +|..|+|.+-|.+.+.. +.++|.|....
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 78999999999999753 26888876544
No 11
>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=89.30 E-value=1.1 Score=30.33 Aligned_cols=42 Identities=24% Similarity=0.366 Sum_probs=30.4
Q ss_pred eEeCCCceeecCCccEEEeeCeEEEEEEecCCCceEEEeeeC
Q 032857 66 RFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVHVEPK 107 (132)
Q Consensus 66 kfhPG~NVg~GrDhTLfAl~~G~V~f~~~~~~~r~~V~V~p~ 107 (132)
+||.|--+.......++|+.+|+|.|.......-.+|.|.-.
T Consensus 1 r~h~Gid~~~~~g~~V~A~~~G~V~~~~~~~~~g~~V~i~~~ 42 (96)
T PF01551_consen 1 RFHNGIDFAAPEGTPVYAPADGKVVFVGEDPGYGNYVIIQHG 42 (96)
T ss_dssp -EE-SEEEEETTT-EEEESSSEEEEEEEEETTTEEEEEEEET
T ss_pred CCeeeEEeCCCCCCEEEeCccEEEEEEEeccCCccEEEEEeC
Confidence 588888888888788999999999998874344666666543
No 12
>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=87.86 E-value=1.5 Score=38.32 Aligned_cols=44 Identities=27% Similarity=0.514 Sum_probs=35.6
Q ss_pred eEEecCcEEee----ccc------------------ceEeCCCceeec-CC-ccEEEeeCeEEEEEEe
Q 032857 51 ERVIPGNIIVR----QRG------------------TRFHPGDYVGMG-KD-HTLYALKEGRVKFEKH 94 (132)
Q Consensus 51 q~V~~G~IIvR----QRG------------------tkfhPG~NVg~G-rD-hTLfAl~~G~V~f~~~ 94 (132)
..|.+|+.|++ +.| ..|.+|+||.+- .| -+|+|.++|++.|...
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 34888888887 334 478899999999 77 4799999999999954
No 13
>COG1315 Uncharacterized conserved protein [Function unknown]
Probab=76.79 E-value=2.7 Score=39.13 Aligned_cols=36 Identities=28% Similarity=0.360 Sum_probs=29.0
Q ss_pred ceEeCCCceeecCC-ccEEEeeCeEEEEEEecCCCceEEEeeeC
Q 032857 65 TRFHPGDYVGMGKD-HTLYALKEGRVKFEKHKLSGRKWVHVEPK 107 (132)
Q Consensus 65 tkfhPG~NVg~GrD-hTLfAl~~G~V~f~~~~~~~r~~V~V~p~ 107 (132)
..|++|+|+- -|| .||.|.++|..-+.+. .|+|+|.
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 8999999999988754 3666653
No 14
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=71.20 E-value=3.8 Score=25.67 Aligned_cols=18 Identities=22% Similarity=0.388 Sum_probs=15.4
Q ss_pred eeeeeCCeEEecCcEEee
Q 032857 44 GVKKFGGERVIPGNIIVR 61 (132)
Q Consensus 44 GiK~~~Gq~V~~G~IIvR 61 (132)
=|..-.|++|++|++|++
T Consensus 15 ~v~V~~G~~VkkGd~L~~ 32 (50)
T PF13533_consen 15 SVYVKEGQQVKKGDVLLV 32 (50)
T ss_pred EEEecCCCEEcCCCEEEE
Confidence 356679999999999987
No 15
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=59.63 E-value=19 Score=39.48 Aligned_cols=64 Identities=23% Similarity=0.431 Sum_probs=43.0
Q ss_pred eeeeCCeEEecCcEEee-cccc----eEeCCC-------ceeecCCccEEEeeCeEEEEE-EecCCCceEEEeeeCCC
Q 032857 45 VKKFGGERVIPGNIIVR-QRGT----RFHPGD-------YVGMGKDHTLYALKEGRVKFE-KHKLSGRKWVHVEPKEG 109 (132)
Q Consensus 45 iK~~~Gq~V~~G~IIvR-QRGt----kfhPG~-------NVg~GrDhTLfAl~~G~V~f~-~~~~~~r~~V~V~p~~~ 109 (132)
+-+.+|+.|.+|+||.| -|-+ -+--|. -...-|+..+.|-++|+|.|- ++ .++++.|.|.+..+
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 122221 134567899999999999983 22 13456677877654
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=55.70 E-value=27 Score=21.19 Aligned_cols=39 Identities=21% Similarity=0.129 Sum_probs=29.4
Q ss_pred eeeeCCeEEecCcEEeecccceEeCCCceeecCCccEEEeeCeEEEEEE
Q 032857 45 VKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEK 93 (132)
Q Consensus 45 iK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V~f~~ 93 (132)
+..-.|++|.+|+.|.+=.-. ..+..|.|..+|+|....
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 667789999999999963221 125679999999997654
No 17
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=50.24 E-value=39 Score=28.54 Aligned_cols=54 Identities=20% Similarity=0.346 Sum_probs=38.4
Q ss_pred eeCCeEEecCcEEeecccceEeCCCceeecCCccEEEeeCeEEEEEEecCCCceEEEeeeCCC
Q 032857 47 KFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVHVEPKEG 109 (132)
Q Consensus 47 ~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V~f~~~~~~~r~~V~V~p~~~ 109 (132)
....+.|.||++|.-+- .|..|.++.+ +|.-++|.+-|.|.++.+. |.|.|.+.
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 45678899999654433 3555555555 8999999999999987542 66666554
No 18
>PF13375 RnfC_N: RnfC Barrel sandwich hybrid domain
Probab=47.60 E-value=27 Score=25.23 Aligned_cols=33 Identities=24% Similarity=0.350 Sum_probs=24.3
Q ss_pred eeCCeEEecCcEEeecccceEeCCCceeecCCccEEEeeCeEEE
Q 032857 47 KFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVK 90 (132)
Q Consensus 47 ~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V~ 90 (132)
+--||+|..|++|.+-.|. + .-.|+|.++|+|.
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 4568999999998876441 1 1268999999994
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=46.30 E-value=28 Score=29.75 Aligned_cols=42 Identities=19% Similarity=0.141 Sum_probs=30.9
Q ss_pred eeeCCeEEecCcEEeecccceEe-CCCceeecCCccEEEeeCeEEEEEEe
Q 032857 46 KKFGGERVIPGNIIVRQRGTRFH-PGDYVGMGKDHTLYALKEGRVKFEKH 94 (132)
Q Consensus 46 K~~~Gq~V~~G~IIvRQRGtkfh-PG~NVg~GrDhTLfAl~~G~V~f~~~ 94 (132)
.+--|+.|.+|++|.+..- +. +|+-+ ++|.|..+|+|.+...
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 44333 6999999999988654
No 20
>PRK05889 putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Provisional
Probab=44.47 E-value=34 Score=22.31 Aligned_cols=40 Identities=20% Similarity=0.212 Sum_probs=29.3
Q ss_pred ceeeeeCCeEEecCcEEeecccceEeCCCceeecCCccEEEeeCeEEEEE
Q 032857 43 LGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFE 92 (132)
Q Consensus 43 LGiK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V~f~ 92 (132)
.=|.+-.|+.|.+|+.|+-=--.| -++.|.|..+|+|.-.
T Consensus 14 ~~~~v~~Gd~V~~g~~l~~ve~~K----------~~~~I~a~~~G~V~~i 53 (71)
T PRK05889 14 LEVVVNEGDQIGKGDTLVLLESMK----------MEIPVLAEVAGTVSKV 53 (71)
T ss_pred EEEEeCCCCEECCCCEEEEEEecc----------ceeEEeCCCCEEEEEE
Confidence 347788899999999998322222 3678999999998643
No 21
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=42.31 E-value=69 Score=35.61 Aligned_cols=65 Identities=20% Similarity=0.320 Sum_probs=44.1
Q ss_pred eeeeCCeEEecCcEEee-cccce----EeCCC-------cee--ecCCccEEEeeCeEEEEEEecCCCceEEEeeeCCCC
Q 032857 45 VKKFGGERVIPGNIIVR-QRGTR----FHPGD-------YVG--MGKDHTLYALKEGRVKFEKHKLSGRKWVHVEPKEGH 110 (132)
Q Consensus 45 iK~~~Gq~V~~G~IIvR-QRGtk----fhPG~-------NVg--~GrDhTLfAl~~G~V~f~~~~~~~r~~V~V~p~~~~ 110 (132)
+-+.+|+.|.+|+||+| .|-+. +--|. -.. .=||..+.|.++|+|+|.++ .++++.|.|.+..++
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 45678999999999998 44321 11121 122 45689999999999999654 245667778777644
No 22
>cd06253 M14_ASTE_ASPA_like_3 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD.
Probab=33.43 E-value=66 Score=26.88 Aligned_cols=41 Identities=20% Similarity=0.216 Sum_probs=28.7
Q ss_pred eeCCeEEecCcEEeecccceEeCCCceeecCCccEEEeeCeEEEEEEe
Q 032857 47 KFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKH 94 (132)
Q Consensus 47 ~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V~f~~~ 94 (132)
+--|+.|.+|++|.+..-. ++|+-+ .++.|+.+|+|-+.+.
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 5899999999988764
No 23
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=33.28 E-value=1.1e+02 Score=25.42 Aligned_cols=62 Identities=21% Similarity=0.298 Sum_probs=41.0
Q ss_pred EEecCcEEeecccceEeCCCceeecCCccEEEeeCeEEEEEEecCCCceEEEeeeCCCCcccccc
Q 032857 52 RVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVHVEPKEGHVLHPLY 116 (132)
Q Consensus 52 ~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V~f~~~~~~~r~~V~V~p~~~~~~hp~~ 116 (132)
+|.||+.+.|--+- +.+|++..- ++..|||-..|.+.++ .-..++..+++.......++|..
T Consensus 7 ~~lpG~~~c~~e~~-~~~g~Gtye-~~~yI~aS~ag~~~~~-~~~~~~~v~~~~~~~~~~~LP~~ 68 (193)
T KOG3409|consen 7 LVLPGEVVCRAEGE-YRMGEGTYE-RNGYIFASVAGVNFRD-NLVQKIEVVSVEKQLFNELLPFV 68 (193)
T ss_pred EEcccceeeecccc-cccccceee-cCCeEEeccccceeec-CCccceeeeeecccchhhcCCcc
Confidence 67888888876652 367777654 3448999999955444 32356677777666656666654
No 24
>PRK09774 fec operon regulator FecR; Reviewed
Probab=32.81 E-value=88 Score=26.15 Aligned_cols=39 Identities=23% Similarity=0.227 Sum_probs=32.6
Q ss_pred EEecCcEEeecccceEeCCCceeecCCccEEEeeCeEEEEEEe
Q 032857 52 RVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKH 94 (132)
Q Consensus 52 ~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V~f~~~ 94 (132)
.|..|..-|+-.||+| ||..-.+.+-+++.+|.|++...
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 3556888888899998 68888888999999999999764
No 25
>COG4687 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.69 E-value=56 Score=25.25 Aligned_cols=41 Identities=22% Similarity=0.519 Sum_probs=36.2
Q ss_pred ecCcEEeecccceEeCCCcee---------------------ecCCccEEEeeCeEEEEEEe
Q 032857 54 IPGNIIVRQRGTRFHPGDYVG---------------------MGKDHTLYALKEGRVKFEKH 94 (132)
Q Consensus 54 ~~G~IIvRQRGtkfhPG~NVg---------------------~GrDhTLfAl~~G~V~f~~~ 94 (132)
.-|-||+=..|+.|++-.||. +||.+.|+-...|.|.|.-+
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 568899999999999988875 78899999999999999865
No 26
>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=32.18 E-value=84 Score=21.17 Aligned_cols=38 Identities=29% Similarity=0.459 Sum_probs=19.3
Q ss_pred ceEeC---CCceeecCCccEEEe----eCeEEEEEEecCCCceEEE
Q 032857 65 TRFHP---GDYVGMGKDHTLYAL----KEGRVKFEKHKLSGRKWVH 103 (132)
Q Consensus 65 tkfhP---G~NVg~GrDhTLfAl----~~G~V~f~~~~~~~r~~V~ 103 (132)
+.||+ |.||-|..|.+.-.- .+| +.|+.++++..-.+.
T Consensus 2 l~FH~~~~G~nV~L~~~~~~A~R~~sf~~g-iVFS~rPl~~~E~~~ 46 (69)
T PF07177_consen 2 LRFHPNVHGKNVRLSNDGTVARRVSSFNNG-IVFSSRPLRIGEKFE 46 (69)
T ss_dssp --EEC-EE-TTEEE-SSS-EEEEST-SSS--EEEESS-B-TT-EEE
T ss_pred ccccCcccCCCEEEcCCCeEEEecccCCce-EEEecCCccCCCEEE
Confidence 46998 999999999975332 234 567776554433333
No 27
>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=31.41 E-value=33 Score=26.84 Aligned_cols=41 Identities=27% Similarity=0.257 Sum_probs=28.2
Q ss_pred EEecCcEEeecccceEeCCCceeecCCccEEEeeCeEEEEEE
Q 032857 52 RVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEK 93 (132)
Q Consensus 52 ~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V~f~~ 93 (132)
.|++|.|.+||+-+.|.|-.. +=|..++.+=+.+-.|....
T Consensus 52 WVikg~i~~RQ~Il~i~~~~~-~dG~~rc~ivL~P~li~v~~ 92 (137)
T PF07370_consen 52 WVIKGQIQCRQRILDIEEVTD-GDGIRRCAIVLDPELIRVEP 92 (137)
T ss_pred EEECCEEEEeeeeeeeeEecC-CCCcccEEEEECCcEEEccc
Confidence 699999999999988877432 11333566666666666654
No 28
>PF13540 RCC1_2: Regulator of chromosome condensation (RCC1) repeat; PDB: 3QI0_D 1JTD_B 3QHY_B.
Probab=31.29 E-value=54 Score=18.43 Aligned_cols=20 Identities=25% Similarity=0.230 Sum_probs=15.9
Q ss_pred eeecCCccEEEeeCeEEEEE
Q 032857 73 VGMGKDHTLYALKEGRVKFE 92 (132)
Q Consensus 73 Vg~GrDhTLfAl~~G~V~f~ 92 (132)
|-.|.+||+.=+.+|.|.--
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 67899999999999998543
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=30.09 E-value=75 Score=20.18 Aligned_cols=39 Identities=23% Similarity=0.246 Sum_probs=27.7
Q ss_pred eeeeCCeEEecCcEEeecccceEeCCCceeecCCccEEEeeCeEEEEEE
Q 032857 45 VKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEK 93 (132)
Q Consensus 45 iK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V~f~~ 93 (132)
+.+-.|+.|.+|+.|..=-..| -...|.|..+|.|.-..
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 6667889999998888732221 14679999999986543
No 30
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=29.57 E-value=2.3e+02 Score=20.83 Aligned_cols=23 Identities=22% Similarity=0.424 Sum_probs=17.7
Q ss_pred ccEEEeeCeEEEEEEecCCCceE
Q 032857 79 HTLYALKEGRVKFEKHKLSGRKW 101 (132)
Q Consensus 79 hTLfAl~~G~V~f~~~~~~~r~~ 101 (132)
..+|-+.+|.|+.+.....++.+
T Consensus 27 ~~~y~I~~G~vr~~~~~~~G~e~ 49 (202)
T PRK13918 27 DMLYRVRSGLVRLHTVDDEGNAL 49 (202)
T ss_pred CeEEEEEeeEEEEEEECCCCCEE
Confidence 67999999999998865444443
No 31
>PRK06549 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=29.45 E-value=74 Score=24.15 Aligned_cols=43 Identities=16% Similarity=0.175 Sum_probs=33.7
Q ss_pred CCccceeeeeCCeEEecCcEEeecccceEeCCCceeecCCccEEEeeCeEEEE
Q 032857 39 KPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKF 91 (132)
Q Consensus 39 ~~KrLGiK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V~f 91 (132)
.++=+=|....|+.|.+|+.|+.=.-+|. ...|.|..+|+|..
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 45556689999999999999997544442 56799999999964
No 32
>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=29.42 E-value=1.4e+02 Score=18.21 Aligned_cols=12 Identities=8% Similarity=0.293 Sum_probs=5.1
Q ss_pred EEEeeCeEEEEE
Q 032857 81 LYALKEGRVKFE 92 (132)
Q Consensus 81 LfAl~~G~V~f~ 92 (132)
++=..+|.+.+.
T Consensus 22 ~~~vl~G~~~~~ 33 (71)
T PF07883_consen 22 FFYVLSGEGTLT 33 (71)
T ss_dssp EEEEEESEEEEE
T ss_pred EEEEEECCEEEE
Confidence 333444444444
No 33
>COG1726 NqrA Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrA [Energy production and conversion]
Probab=28.41 E-value=1.3e+02 Score=27.74 Aligned_cols=58 Identities=21% Similarity=0.267 Sum_probs=44.2
Q ss_pred CCCCCCccceeeeeCCeEEecCcEEeecccceEeCCCceeecCCccEEEeeCeEEEEEEecCCCceEEEe
Q 032857 35 GRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGRKWVHV 104 (132)
Q Consensus 35 GrdS~~KrLGiK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V~f~~~~~~~r~~V~V 104 (132)
|++=.|-|+++|+..|+.|++|++|+-- |-.||. -+-|+++|.|.=-++. .+|..-+|
T Consensus 33 g~ey~gmrp~mkV~~gD~VkkGq~LfEd---Kknpgv--------~~Tap~sG~V~aI~RG-~KRvLqsV 90 (447)
T COG1726 33 GEEYVGMRPSMKVREGDAVKKGQVLFED---KKNPGV--------VFTAPVSGKVTAIHRG-EKRVLQSV 90 (447)
T ss_pred cccccCCCCcceeccCCeeeccceeeec---ccCCCe--------EEeccCCceEEEeecc-cceeeeeE
Confidence 7777899999999999999999999864 344552 2459999999766654 46665554
No 34
>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=27.66 E-value=39 Score=26.45 Aligned_cols=17 Identities=29% Similarity=0.528 Sum_probs=10.5
Q ss_pred eeeeCCeEEecCcEEee
Q 032857 45 VKKFGGERVIPGNIIVR 61 (132)
Q Consensus 45 iK~~~Gq~V~~G~IIvR 61 (132)
|-+-+||+|++|++|++
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 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=26.40 E-value=48 Score=25.04 Aligned_cols=41 Identities=29% Similarity=0.499 Sum_probs=33.3
Q ss_pred CCeEEecCcEEeecccceEeCCCceeecCCccEEEeeCeEE
Q 032857 49 GGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRV 89 (132)
Q Consensus 49 ~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V 89 (132)
.+...-=|.++||.-.--+--|.||+.|..-|+|++.+-.|
T Consensus 14 ~~nW~dLGtLvv~KeedgI~tgLN~~~GhsatfFsleesEv 54 (108)
T PF02471_consen 14 SGNWTDLGTLVVRKEEDGIETGLNVGGGHSATFFSLEESEV 54 (108)
T ss_pred CCCceeeeeEEEEeecCceeeccccCCCceEEEEEecHHHH
Confidence 45566668888998888899999999999999999876544
No 36
>PRK14875 acetoin dehydrogenase E2 subunit dihydrolipoyllysine-residue acetyltransferase; Provisional
Probab=26.31 E-value=78 Score=25.23 Aligned_cols=42 Identities=17% Similarity=0.175 Sum_probs=31.2
Q ss_pred CCccceeeeeCCeEEecCcEEeecccceEeCCCceeecCCccEEEeeCeEEE
Q 032857 39 KPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVK 90 (132)
Q Consensus 39 ~~KrLGiK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V~ 90 (132)
.++=.-|.+-.|+.|.+|++|+.--.. --.+.+-|+.+|+|.
T Consensus 16 ~g~~~~~~~~~g~~v~~~~~~~~~e~~----------k~~~~~~a~~~g~~~ 57 (371)
T PRK14875 16 EGKVAGWLVQEGDEVEKGDELLDVETD----------KITNEVEAPAAGTLR 57 (371)
T ss_pred eEEEEEEEcCCCCEeCCCCEEEEEEec----------ceeEEEecCCCeEEE
Confidence 455556788899999999999982222 224778899999986
No 37
>PRK08225 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=25.55 E-value=1.1e+02 Score=19.58 Aligned_cols=39 Identities=21% Similarity=0.181 Sum_probs=28.2
Q ss_pred ceeeeeCCeEEecCcEEeecccceEeCCCceeecCCccEEEeeCeEEEE
Q 032857 43 LGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKF 91 (132)
Q Consensus 43 LGiK~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V~f 91 (132)
.-|..-.|+.|.+|+.|..=.-.| -...+.|..+|+|.-
T Consensus 13 ~~~~v~~G~~V~~g~~l~~ve~~k----------~~~~v~s~~~G~v~~ 51 (70)
T PRK08225 13 WKIVVKVGDTVEEGQDVVILESMK----------MEIPIVAEEAGTVKK 51 (70)
T ss_pred EEEEeCCCCEECCCCEEEEEEcCC----------CcceEeCCCCEEEEE
Confidence 336777799999999998732222 267799999998853
No 38
>PRK00807 50S ribosomal protein L24e; Validated
Probab=25.29 E-value=67 Score=20.77 Aligned_cols=23 Identities=26% Similarity=0.541 Sum_probs=16.6
Q ss_pred cceEeCCCceeecCCccEEEeeCeEEEEEE
Q 032857 64 GTRFHPGDYVGMGKDHTLYALKEGRVKFEK 93 (132)
Q Consensus 64 GtkfhPG~NVg~GrDhTLfAl~~G~V~f~~ 93 (132)
|.+++||.+. +|...||.|.+..
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 7789999874 4566777776654
No 39
>PRK11637 AmiB activator; Provisional
Probab=25.02 E-value=1.1e+02 Score=26.49 Aligned_cols=47 Identities=21% Similarity=0.449 Sum_probs=29.2
Q ss_pred eeCCeEEec--CcEEeecccceEe-----CCCceeecCCccEEEeeCeEEEEEEe
Q 032857 47 KFGGERVIP--GNIIVRQRGTRFH-----PGDYVGMGKDHTLYALKEGRVKFEKH 94 (132)
Q Consensus 47 ~~~Gq~V~~--G~IIvRQRGtkfh-----PG~NVg~GrDhTLfAl~~G~V~f~~~ 94 (132)
...|.+.+| |.|+ ..=|...+ .|--+.-..+-.++|..+|+|.|...
T Consensus 302 ~~~g~~~~Pv~g~i~-~~fg~~~~~~~~~~Gi~i~~~~g~~v~A~~~G~V~~~~~ 355 (428)
T PRK11637 302 RPRGQAFWPVRGPTL-HRFGEQLQGELRWKGMVIGASEGTEVKAIADGRVLLADW 355 (428)
T ss_pred CCCCCCccCCCCCcc-CCCCCCCCCCCCCCCEEeecCCCCeEEecCCeEEEEeec
Confidence 334555555 6543 44454444 44444444667899999999999753
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=23.11 E-value=56 Score=22.37 Aligned_cols=20 Identities=35% Similarity=0.599 Sum_probs=15.1
Q ss_pred eeeeCCeEEecCcEEeeccc
Q 032857 45 VKKFGGERVIPGNIIVRQRG 64 (132)
Q Consensus 45 iK~~~Gq~V~~G~IIvRQRG 64 (132)
+.+.||+.|.+|++|++=+|
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 34579999999999998776
No 41
>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=22.88 E-value=1.6e+02 Score=23.98 Aligned_cols=27 Identities=19% Similarity=0.449 Sum_probs=21.3
Q ss_pred eCeEEEEEEecCCCceEEEeeeCCCCcc
Q 032857 85 KEGRVKFEKHKLSGRKWVHVEPKEGHVL 112 (132)
Q Consensus 85 ~~G~V~f~~~~~~~r~~V~V~p~~~~~~ 112 (132)
..|.|++..+ ..++.||.|+|++.+++
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 4678888876 57899999999966554
No 42
>COG5455 Predicted integral membrane protein [Function unknown]
Probab=22.36 E-value=87 Score=24.40 Aligned_cols=18 Identities=33% Similarity=0.477 Sum_probs=15.9
Q ss_pred eeecCCccEEEeeCeEEEE
Q 032857 73 VGMGKDHTLYALKEGRVKF 91 (132)
Q Consensus 73 Vg~GrDhTLfAl~~G~V~f 91 (132)
|.+|-|+-|.+..+| |-|
T Consensus 106 vrvg~dyvLi~~~tG-lI~ 123 (129)
T COG5455 106 VRVGGDYVLISDTTG-LIF 123 (129)
T ss_pred EEECCeEEEEeecCc-eEE
Confidence 899999999999999 444
No 43
>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=21.88 E-value=1.1e+02 Score=25.23 Aligned_cols=40 Identities=18% Similarity=0.178 Sum_probs=27.0
Q ss_pred eeCCeEEecCcEEeecccceEeCCCceeecCCccEEEeeCeEEEEEEe
Q 032857 47 KFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKH 94 (132)
Q Consensus 47 ~~~Gq~V~~G~IIvRQRGtkfhPG~NVg~GrDhTLfAl~~G~V~f~~~ 94 (132)
+--|+.|.+|++|.+..-. -| ....++.|+.+|.|.+...
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 4457888888888775431 11 1126899999999976554
No 44
>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=20.72 E-value=81 Score=19.04 Aligned_cols=21 Identities=24% Similarity=0.610 Sum_probs=17.1
Q ss_pred CeEEecCcEEeecccceEeCC
Q 032857 50 GERVIPGNIIVRQRGTRFHPG 70 (132)
Q Consensus 50 Gq~V~~G~IIvRQRGtkfhPG 70 (132)
++.|.++.++++..|..|||-
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 45
>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=20.34 E-value=74 Score=25.87 Aligned_cols=19 Identities=21% Similarity=0.373 Sum_probs=11.5
Q ss_pred ceeeeeCCeEEecCcEEee
Q 032857 43 LGVKKFGGERVIPGNIIVR 61 (132)
Q Consensus 43 LGiK~~~Gq~V~~G~IIvR 61 (132)
.-|-+-.|+.|.+|++|++
T Consensus 28 ~~i~V~eG~~V~~G~~L~~ 46 (327)
T TIGR02971 28 KKLLVAEGDRVQAGQVLAE 46 (327)
T ss_pred EEEEccCCCEecCCcEEEE
Confidence 3455556666666666665
Done!