Query 022009
Match_columns 304
No_of_seqs 226 out of 771
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 07:19:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022009.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022009hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2086 Protein tyrosine phosp 100.0 6.4E-73 1.4E-77 539.1 21.3 285 17-304 79-379 (380)
2 smart00553 SEP Domain present 100.0 2.2E-35 4.7E-40 234.1 9.0 88 115-202 2-90 (93)
3 PF08059 SEP: SEP domain; Int 100.0 1E-30 2.3E-35 200.1 6.4 74 120-193 1-75 (75)
4 cd01770 p47_UBX p47-like ubiqu 99.9 5.7E-25 1.2E-29 170.1 10.0 76 228-304 2-78 (79)
5 cd01767 UBX UBX (ubiquitin reg 99.8 1.1E-20 2.4E-25 144.8 9.7 74 229-304 1-76 (77)
6 smart00166 UBX Domain present 99.8 4.6E-19 9.9E-24 136.8 10.0 76 228-304 2-80 (80)
7 cd01773 Faf1_like1_UBX Faf1 ik 99.8 7.2E-19 1.6E-23 136.7 10.0 73 227-301 2-77 (82)
8 cd01774 Faf1_like2_UBX Faf1 ik 99.8 1.2E-18 2.7E-23 136.5 9.3 69 228-298 2-77 (85)
9 cd01771 Faf1_UBX Faf1 UBX doma 99.8 2.1E-18 4.5E-23 133.8 9.7 73 227-301 1-76 (80)
10 cd01772 SAKS1_UBX SAKS1-like U 99.7 6.3E-18 1.4E-22 130.5 9.3 73 229-303 3-79 (79)
11 PF00789 UBX: UBX domain; Int 99.7 4.4E-18 9.5E-23 131.3 8.1 78 226-304 2-82 (82)
12 KOG2689 Predicted ubiquitin re 99.4 8.8E-13 1.9E-17 121.9 10.0 77 227-304 207-286 (290)
13 KOG1364 Predicted ubiquitin re 99.0 3.1E-10 6.7E-15 108.3 4.2 74 230-304 277-355 (356)
14 KOG2507 Ubiquitin regulatory p 98.9 1.5E-09 3.2E-14 105.8 4.8 69 228-297 312-382 (506)
15 KOG1363 Predicted regulator of 98.4 5.5E-07 1.2E-11 90.2 6.8 74 227-302 380-457 (460)
16 cd01796 DDI1_N DNA damage indu 97.3 0.00081 1.7E-08 50.5 6.8 68 233-303 1-70 (71)
17 cd01807 GDX_N ubiquitin-like d 97.1 0.0022 4.7E-08 48.3 7.4 66 232-301 2-68 (74)
18 cd01806 Nedd8 Nebb8-like ubiq 97.1 0.003 6.6E-08 47.0 7.7 65 232-300 2-67 (76)
19 cd01794 DC_UbP_C dendritic cel 97.1 0.0018 4E-08 48.7 6.4 65 233-301 1-65 (70)
20 cd01792 ISG15_repeat1 ISG15 ub 97.0 0.0046 1E-07 47.3 8.0 68 231-300 3-71 (80)
21 cd01804 midnolin_N Ubiquitin-l 97.0 0.0045 9.7E-08 47.4 7.6 65 232-301 3-68 (78)
22 PF00240 ubiquitin: Ubiquitin 96.8 0.0038 8.2E-08 45.9 6.0 62 236-301 1-63 (69)
23 cd01809 Scythe_N Ubiquitin-lik 96.8 0.0071 1.5E-07 44.5 7.4 66 232-301 2-68 (72)
24 cd01791 Ubl5 UBL5 ubiquitin-li 96.7 0.013 2.8E-07 44.5 8.4 67 231-301 2-69 (73)
25 cd01805 RAD23_N Ubiquitin-like 96.7 0.011 2.3E-07 44.4 7.7 66 232-301 2-70 (77)
26 cd01803 Ubiquitin Ubiquitin. U 96.6 0.011 2.3E-07 44.0 7.1 65 232-300 2-67 (76)
27 PF12090 Spt20: Spt20 family; 96.6 0.0022 4.8E-08 57.1 3.8 58 116-174 14-82 (182)
28 PTZ00044 ubiquitin; Provisiona 96.6 0.011 2.4E-07 44.3 7.1 65 232-300 2-67 (76)
29 cd01798 parkin_N amino-termina 96.6 0.0094 2E-07 44.2 6.6 64 233-300 1-65 (70)
30 cd01814 NTGP5 Ubiquitin-like N 96.5 0.0064 1.4E-07 50.1 5.7 62 229-294 3-72 (113)
31 cd01810 ISG15_repeat2 ISG15 ub 96.5 0.011 2.4E-07 44.4 6.6 64 233-300 1-65 (74)
32 cd01808 hPLIC_N Ubiquitin-like 96.4 0.018 4E-07 42.8 7.1 66 232-302 2-68 (71)
33 PF11543 UN_NPL4: Nuclear pore 96.2 0.0063 1.4E-07 47.2 4.1 66 231-298 5-72 (80)
34 smart00213 UBQ Ubiquitin homol 96.2 0.022 4.7E-07 40.5 6.4 61 232-297 2-62 (64)
35 cd01812 BAG1_N Ubiquitin-like 96.0 0.037 8.1E-07 40.7 7.2 65 232-301 2-67 (71)
36 PF13881 Rad60-SLD_2: Ubiquiti 95.9 0.031 6.7E-07 46.0 6.8 63 230-296 2-72 (111)
37 cd01769 UBL Ubiquitin-like dom 95.6 0.065 1.4E-06 38.5 7.1 64 235-302 2-66 (69)
38 cd01802 AN1_N ubiquitin-like d 95.6 0.072 1.6E-06 43.1 7.9 69 228-300 25-94 (103)
39 cd01797 NIRF_N amino-terminal 95.4 0.085 1.8E-06 40.4 7.4 66 232-301 2-70 (78)
40 cd01763 Sumo Small ubiquitin-r 95.0 0.19 4.2E-06 39.1 8.5 67 227-297 8-74 (87)
41 TIGR00601 rad23 UV excision re 94.9 0.1 2.2E-06 51.5 8.0 66 232-301 2-71 (378)
42 PF11976 Rad60-SLD: Ubiquitin- 93.9 0.25 5.3E-06 36.5 6.4 62 232-297 2-64 (72)
43 cd01793 Fubi Fubi ubiquitin-li 93.9 0.29 6.3E-06 36.6 6.8 63 232-300 2-65 (74)
44 cd01790 Herp_N Homocysteine-re 93.6 0.33 7.3E-06 37.6 6.8 60 231-294 2-65 (79)
45 cd01800 SF3a120_C Ubiquitin-li 93.6 0.23 4.9E-06 37.5 5.8 59 239-301 6-65 (76)
46 cd01813 UBP_N UBP ubiquitin pr 93.3 0.56 1.2E-05 35.5 7.5 68 232-301 2-70 (74)
47 cd00196 UBQ Ubiquitin-like pro 91.9 0.34 7.3E-06 32.1 4.4 60 234-297 1-60 (69)
48 cd01799 Hoil1_N Ubiquitin-like 89.9 1 2.3E-05 34.2 5.8 57 236-296 8-64 (75)
49 KOG0011 Nucleotide excision re 89.1 1 2.3E-05 43.6 6.4 69 232-303 2-72 (340)
50 PF14560 Ubiquitin_2: Ubiquiti 88.8 1.9 4E-05 33.3 6.6 69 231-299 2-76 (87)
51 cd01795 USP48_C USP ubiquitin- 87.5 1.6 3.6E-05 35.4 5.6 55 243-302 17-74 (107)
52 PLN02560 enoyl-CoA reductase 86.5 3.9 8.5E-05 39.4 8.7 71 232-303 2-81 (308)
53 PF14836 Ubiquitin_3: Ubiquiti 85.7 3.4 7.3E-05 32.8 6.4 56 242-298 15-72 (88)
54 PF08817 YukD: WXG100 protein 85.5 2.9 6.2E-05 31.8 5.9 69 230-301 2-77 (79)
55 PF11470 TUG-UBL1: GLUT4 regul 82.3 4.5 9.8E-05 30.1 5.6 60 237-300 3-63 (65)
56 cd01801 Tsc13_N Ubiquitin-like 82.2 9.1 0.0002 28.8 7.4 54 248-303 20-75 (77)
57 PF09379 FERM_N: FERM N-termin 81.2 1.7 3.6E-05 32.5 3.0 62 235-296 1-65 (80)
58 cd01789 Alp11_N Ubiquitin-like 80.7 9.4 0.0002 29.4 7.1 65 231-297 2-72 (84)
59 cd01815 BMSC_UbP_N Ubiquitin-l 79.7 5.8 0.00013 30.5 5.5 49 248-300 18-70 (75)
60 smart00295 B41 Band 4.1 homolo 77.9 6.9 0.00015 33.9 6.3 64 231-295 4-71 (207)
61 KOG3493 Ubiquitin-like protein 67.6 4.8 0.0001 30.2 2.3 24 240-263 11-34 (73)
62 cd01777 SNX27_RA Ubiquitin dom 66.6 11 0.00024 29.8 4.3 34 231-264 2-35 (87)
63 cd01787 GRB7_RA RA (RAS-associ 66.2 25 0.00053 27.7 6.2 55 231-286 3-62 (85)
64 cd01760 RBD Ubiquitin-like dom 59.6 27 0.00059 26.4 5.2 43 233-275 2-44 (72)
65 cd01818 TIAM1_RBD Ubiquitin do 51.0 40 0.00087 26.1 4.9 41 235-275 4-44 (77)
66 PF02196 RBD: Raf-like Ras-bin 49.9 67 0.0015 24.0 6.0 52 232-284 2-53 (71)
67 PF13019 Telomere_Sde2: Telome 48.1 76 0.0017 27.9 6.9 51 232-284 2-57 (162)
68 KOG0010 Ubiquitin-like protein 46.6 46 0.00099 34.2 5.9 63 230-297 15-77 (493)
69 smart00455 RBD Raf-like Ras-bi 45.5 64 0.0014 24.1 5.3 42 233-274 2-43 (70)
70 PF10302 DUF2407: DUF2407 ubiq 42.5 86 0.0019 25.1 5.9 53 232-287 2-59 (97)
71 smart00666 PB1 PB1 domain. Pho 35.1 1.3E+02 0.0029 22.1 5.7 43 231-274 2-44 (81)
72 cd06536 CIDE_N_ICAD CIDE_N dom 34.1 21 0.00046 27.8 1.1 18 117-134 42-59 (80)
73 smart00537 DCX Domain in the D 33.6 42 0.0009 26.2 2.7 35 117-151 5-42 (89)
74 PF00564 PB1: PB1 domain; Int 32.5 1.1E+02 0.0024 22.6 4.9 45 230-274 1-45 (84)
75 KOG0005 Ubiquitin-like protein 30.9 1.5E+02 0.0033 22.0 5.0 65 233-301 3-67 (70)
76 cd01817 RGS12_RBD Ubiquitin do 30.1 1.8E+02 0.0039 22.3 5.6 58 234-292 3-62 (73)
77 cd01615 CIDE_N CIDE_N domain, 30.1 27 0.00059 27.1 1.1 18 117-134 40-57 (78)
78 smart00266 CAD Domains present 29.7 27 0.00057 26.9 1.0 19 117-135 38-56 (74)
79 PF00788 RA: Ras association ( 28.5 1.9E+02 0.0042 21.4 5.7 58 230-288 2-69 (93)
80 PF03562 MltA: MltA specific i 28.2 90 0.0019 27.3 4.1 32 234-266 89-142 (158)
81 cd06538 CIDE_N_FSP27 CIDE_N do 27.2 30 0.00064 26.9 0.9 17 118-134 40-56 (79)
82 COG5100 NPL4 Nuclear pore prot 26.8 2.3E+02 0.0049 28.8 7.0 66 233-303 3-77 (571)
83 cd01788 ElonginB Ubiquitin-lik 25.2 2.9E+02 0.0062 23.1 6.3 51 242-296 13-63 (119)
84 cd00291 SirA_YedF_YeeD SirA, Y 23.4 1.2E+02 0.0026 21.5 3.6 27 237-263 23-49 (69)
85 cd01768 RA RA (Ras-associating 22.3 3.2E+02 0.0069 20.4 5.9 58 233-291 2-68 (87)
86 KOG0625 Phosphoglucomutase [Ca 21.1 37 0.0008 34.5 0.4 35 232-266 485-520 (558)
87 PF01206 TusA: Sulfurtransfera 20.7 1.2E+02 0.0025 21.9 3.0 27 237-263 24-50 (70)
88 PF07872 DUF1659: Protein of u 20.4 1.2E+02 0.0026 20.8 2.8 31 230-260 5-45 (47)
No 1
>KOG2086 consensus Protein tyrosine phosphatase SHP1/Cofactor for p97 ATPase-mediated vesicle membrane fusion [Nuclear structure]
Probab=100.00 E-value=6.4e-73 Score=539.05 Aligned_cols=285 Identities=49% Similarity=0.811 Sum_probs=239.0
Q ss_pred CCccccccccCCCCCCCCCCCCCCCcccccCCccccceeCCCCCC--CchHHHHHHHHHHcCCCCCCCCCCCCCCCCCcc
Q 022009 17 GGIRTLSDLNRRSGPDSDSDDDAPQEYYTGGEKSGMLVQDPSKGD--PNDVDAIFNQAKELGAVEGPLEHLSPSSSSRSF 94 (304)
Q Consensus 17 ~~~~tl~dl~~~~~~~~~~d~~~~q~~yaGGe~SG~~V~~P~~~~--~~~v~~if~~A~~~g~~~~~~~~~~~~~~~~~F 94 (304)
++|+|++|+..+.+.+.++|+++.|+||||||+|||+|..|+++. .+.|+++|++|+++|+.+.... ..-.....|
T Consensus 79 ~~~~s~~d~~~~~~~~~~sddd~~qe~~~gge~~gq~~v~~~~k~~~~e~v~~~~~~a~q~~a~~~~~~--~~~~~~~~~ 156 (380)
T KOG2086|consen 79 TGITSFRDLFSDRDEELESDDDQEQEFYAGGEKSGQMVVEPPDKKSSEEDVDEIFGQARQMGAVEGPLA--PSESSSGEF 156 (380)
T ss_pred cCcCCHHHhccccccccccccchhhhhhhccccccccccCCCccccHHHHHHHHHhhhcccCccccCcc--Ccccccccc
Confidence 689999999876555556677777899999999997777776643 4789999999999999764421 111233567
Q ss_pred cccceecCCccCCCCC-------CCCCCceEEEEEeccceeecCCCCccCCChhhHHHHHHHHcCCCCccccCCCCCCce
Q 022009 95 TGTARLLSGETVPSAP-------QQPEPIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSV 167 (304)
Q Consensus 95 ~G~G~~LG~~~~p~~~-------~~~~~v~~~It~w~nGF~VdDGpfR~yddP~n~~FL~~I~~G~~P~EL~~~~~~~~V 167 (304)
.|++.-|.++.+|... ..++++.|+|+||+|||+|||||||+|+||+|++||++|++|+||.||+.++++++|
T Consensus 157 ~gs~~~lsg~~~~~~~q~~~~~~~~~~~v~~~l~lW~nGFsvdDGplr~ydDP~N~~fL~~I~~Ge~P~eL~~~~~~~~V 236 (380)
T KOG2086|consen 157 LGSGGDLSGEVVPLGTQQQQREAQPPEPVTVTLKLWKNGFSVDDGPLRSYDDPANAEFLESIRKGEAPSELLPVDPGQEV 236 (380)
T ss_pred ccccccccCccccCCcccCcccccCCCcceeEEEEeeccccccCCCcccccChhHHHHHHHHhccCCCHHHhccccCCcc
Confidence 8888877776666532 236779999999999999999999999999999999999999999999999999999
Q ss_pred EEEEee-ccccCCCCCCCCCcccccccccccCCCCCCCCCC-CC--C-CCC-CCCCCCCCcccCCCCCceeEEEEcCCCC
Q 022009 168 HVNLIR-RDVKCPEPEKHHVPFQGVGRTLGSSSTAASEPTV-DS--T-PVN-TASSSSEGLVVDENLPSTSVQIRLADGT 241 (304)
Q Consensus 168 ~v~v~~-r~e~y~~~~~~~~~F~G~G~~LGs~~p~~~~~~~-~~--~-~~~-~~~~~~~~~~vd~~~p~t~IqIRl~dG~ 241 (304)
+|+|.| |+|.|.++++.+++|+|+||+||++.|....++. +. + +.+ ..+.+...+.+|+.+|+|+|||||+||+
T Consensus 237 ~v~v~~~r~E~~~~~~~~~~pF~G~Gq~LGs~~p~~~~ss~~~~~~~~p~~~~~~~~~~sl~~d~~~PtTsIQIRLanG~ 316 (380)
T KOG2086|consen 237 DVKVEDHRDEDYLEPKPVFKPFSGEGQRLGSTAPGVSGSSSPPLTATVPANTQERSASSSLVIDPAEPTTSIQIRLANGT 316 (380)
T ss_pred ceeccccccccccCCCcccCCCCCcCeecCCcCCCccccCCCcccccCCccccccccccccccCCCCCcceEEEEecCCc
Confidence 999995 7999999999999999999999998777433221 11 1 111 2234566788999999999999999999
Q ss_pred EEEEecCCCCCHHHHHHHHHhhCCCC-CCCeEEEecCCCCccccCCCCchhhhCCCCeeEEeeC
Q 022009 242 RLIAHFNLHHTISDIHSFIDASRPGT-ARNYQLQMMGFPPKVLADRTQTIEQAGLANSVVIQKF 304 (304)
Q Consensus 242 rl~~rFn~s~TV~dvr~fv~~~~~~~-~~~f~L~t~~fP~k~l~d~s~TL~eagL~na~ivqk~ 304 (304)
|++++||++|||.|||.||..++|.+ ..+|.|++ +||+|+|+|+++||++|||+|+||||||
T Consensus 317 RlV~~fN~sHTv~DIR~fI~~aRp~~~~~~F~L~~-~FPpk~l~D~sqTle~AgL~Nsvlvqr~ 379 (380)
T KOG2086|consen 317 RLVLKFNHSHTVSDIREFIDTARPGDSSTYFILMM-AFPPKPLSDDSQTLEEAGLLNSVLVQRL 379 (380)
T ss_pred eeeeeccCcccHHHHHHHHHhcCCCCcCCceeeee-cCCCcccCCcchhHHhccchhhhhhhhc
Confidence 99999999999999999999999988 56788886 9999999999999999999999999997
No 2
>smart00553 SEP Domain present in Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47.
Probab=100.00 E-value=2.2e-35 Score=234.11 Aligned_cols=88 Identities=47% Similarity=0.828 Sum_probs=83.5
Q ss_pred CceEEEEEeccceeecCCCCccCCChhhHHHHHHHHcCCCCccccCCCCCCceEEEEee-ccccCCCCCCCCCccccccc
Q 022009 115 PIVHNIVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHVNLIR-RDVKCPEPEKHHVPFQGVGR 193 (304)
Q Consensus 115 ~v~~~It~w~nGF~VdDGpfR~yddP~n~~FL~~I~~G~~P~EL~~~~~~~~V~v~v~~-r~e~y~~~~~~~~~F~G~G~ 193 (304)
++.|+||||+|||+|||||||+||||+|++||++|++|+||.||++.++++.|+|+|+| |+|+|++|++++++|+|+||
T Consensus 2 ~v~~~ltlw~nGFtVdDGplr~yddP~N~~FL~~I~~G~~P~EL~~~~~~~~V~v~l~d~~~E~y~~p~~~~~~F~G~G~ 81 (93)
T smart00553 2 KVIVVLTFWSNGFSVDDGPLRTYDDPENAEFLESIRRGEAPLELLRVDKGQPVNVDVEDHRDEDYVAPPKAFKPFSGSGQ 81 (93)
T ss_pred CeEEEEEEecCCcEecCCCcccCCCHhHHHHHHHHHcCCCCHHHHhhcCCCcEEEEeEeccCccccCCCCCccCCccCCc
Confidence 47899999999999999999999999999999999999999999999999999999995 68999999888999999999
Q ss_pred ccccCCCCC
Q 022009 194 TLGSSSTAA 202 (304)
Q Consensus 194 ~LGs~~p~~ 202 (304)
+||+++|..
T Consensus 82 ~LGs~~p~~ 90 (93)
T smart00553 82 KLGSPGPQS 90 (93)
T ss_pred cCCCCCCCc
Confidence 999998875
No 3
>PF08059 SEP: SEP domain; InterPro: IPR012989 The SEP (after shp1, eyc and p47) domain is an eukaryotic domain, which occurs frequently and mainly in single units. Almost all proteins containing a SEP domain are succeeded closely by a UBX domain (see PDOC50033 from PROSITEDOC). The function of the SEP domain is as yet unknown but it has been proposed to act as a reversible competitive inhibitor of the lysosomal cysteine protease cathepsin L [, ]. The sructure of the SEP domain comprises a beta-sheet composed of four strands, and two alpha-helices. One side of the beta-sheet faces alpha1 and alpha2. The longer helix alpha1 packs against the four- stranded beta-sheet, where as the shorter helix alpha2 is located at one edge of the globular structure formed by alpha1 and the four stranded beta sheet. A number of highly conserved hydrophobic residues are present in the SEP domain, which are predominantly buried and form the hydrophobic core [, ]. Some proteins known to contain a SEP domain are listed below: - Eukaryotic NSFL1 cofactor p37 (or p97 cofactor p37), an adapter protein required for Golgi and endoplasmic reticulum biogenesis. It is involved in Golgi and endoplasmic reticulum maintenance during interphase and in their reassembly at the end of mitosis. - Eukaryotic NSFL1 cofactor p47 (or p97 cofactor p47), a major adaptor molecule of the cytosolic AAA-type ATPase (ATPases associated with various cellular activities) p97. p47 is required for the p97-regulated membrane reassembly of the endoplasmic reticulum (ER), the nuclear envelope and the Golgi apparatus. - Vertebrate UBX domain-containing protein 4 (UBXD4). - Plant UBA and UBX domain-containing protein. - Saccharomyces cerevisiae (Baker's yeast) UBX domain-containing protein 1 or Suppressor of high-copy PP1 protein (shp1), the homologue of p47. - Drosophila melanogaster (Fruit fly) eyes closed (eyc). ; PDB: 1S3S_G 1VAZ_A 1SS6_A.
Probab=99.96 E-value=1e-30 Score=200.15 Aligned_cols=74 Identities=50% Similarity=0.855 Sum_probs=65.6
Q ss_pred EEEeccceeecCCCCccCCChhhHHHHHHHHcCCCCccccCCCCCCceEEEEeec-cccCCCCCCCCCccccccc
Q 022009 120 IVFWANGFTVNDGPLRRLDDPENASFLESIKKSECPKELEPADKRSSVHVNLIRR-DVKCPEPEKHHVPFQGVGR 193 (304)
Q Consensus 120 It~w~nGF~VdDGpfR~yddP~n~~FL~~I~~G~~P~EL~~~~~~~~V~v~v~~r-~e~y~~~~~~~~~F~G~G~ 193 (304)
||||+|||+|||||||+|+||+|++||++|++|++|.||+..+|+++|+|+|++| +|+|+++++++++|+|+||
T Consensus 1 l~~w~nGf~VddGplR~y~dp~n~~Fl~~I~~G~~P~EL~~~~p~~~v~v~l~d~~~e~y~~~~~~~~~F~G~G~ 75 (75)
T PF08059_consen 1 LTFWRNGFTVDDGPLRPYDDPENAQFLEDINRGYFPSELQQRYPGDGVDVNLEDRRDEDYVPPKKKFKPFSGQGH 75 (75)
T ss_dssp EEEETTEEEETTS-EEETTSTTCHHHHHHHHHT--SCHHHCTTSSS-EEEEEEEECTTSS-SSSSSSTTS-SSSS
T ss_pred CEEecCceEecCCCcccCCCHhHHHHHHHHHhcCCCHHHHhccCCCeEEEEEEeCCCCccCCCCccccCCCcCCC
Confidence 7999999999999999999999999999999999999999999999999999965 8999999999999999997
No 4
>cd01770 p47_UBX p47-like ubiquitin domain. p47_UBX p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events. p47 has carboxy-terminal SEP and UBX domains. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=99.92 E-value=5.7e-25 Score=170.06 Aligned_cols=76 Identities=46% Similarity=0.773 Sum_probs=71.8
Q ss_pred CCceeEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCC-CCCeEEEecCCCCccccCCCCchhhhCCCCeeEEeeC
Q 022009 228 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGT-ARNYQLQMMGFPPKVLADRTQTIEQAGLANSVVIQKF 304 (304)
Q Consensus 228 ~p~t~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~-~~~f~L~t~~fP~k~l~d~s~TL~eagL~na~ivqk~ 304 (304)
+|+|+||||||||+|+++|||.+|||++||+||..+.++. ..+|.|++ +||+|+|++.++||+||||+||+|+|||
T Consensus 2 ~p~t~iqiRlpdG~r~~~rF~~~~tv~~l~~~v~~~~~~~~~~~f~L~t-~fP~k~l~~~~~Tl~eagL~~s~v~q~~ 78 (79)
T cd01770 2 EPTTSIQIRLADGKRLVQKFNSSHRVSDVRDFIVNARPEFAARPFTLMT-AFPVKELSDESLTLKEANLLNAVIVQRL 78 (79)
T ss_pred CCeeEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHhCCCCCCCCEEEec-CCCCcccCCCCCcHHHCCCcCcEEEEEe
Confidence 6899999999999999999999999999999999887654 68999997 9999999988999999999999999998
No 5
>cd01767 UBX UBX (ubiquitin regulatory X) domain. The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation.
Probab=99.84 E-value=1.1e-20 Score=144.75 Aligned_cols=74 Identities=43% Similarity=0.779 Sum_probs=68.5
Q ss_pred CceeEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccC--CCCchhhhCCCCeeEEeeC
Q 022009 229 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLAD--RTQTIEQAGLANSVVIQKF 304 (304)
Q Consensus 229 p~t~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d--~s~TL~eagL~na~ivqk~ 304 (304)
|+|+||||||||+|++++|+.++||++||+||..+... ..+|.|++ +||+|.|++ .++||+||||+|++++|+|
T Consensus 1 p~t~i~iRlpdG~~~~~~F~~~~tl~~l~~fv~~~~~~-~~~f~L~t-~~Pr~~~~~~~~~~TL~e~gL~~s~~~~~~ 76 (77)
T cd01767 1 PTTKIQIRLPDGKRLEQRFNSTHKLSDVRDFVESNGPP-AEPFTLMT-SFPRRVLTDLDYELTLQEAGLVNEVVFQRL 76 (77)
T ss_pred CcEEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHcCCC-CCCEEEEe-CCCCccCCCCCccCcHHHcCCccceEEEEe
Confidence 68999999999999999999999999999999987644 57899997 999999986 7999999999999999987
No 6
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=99.79 E-value=4.6e-19 Score=136.79 Aligned_cols=76 Identities=24% Similarity=0.422 Sum_probs=67.4
Q ss_pred CCceeEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCC--CCchhhhCCCC-eeEEeeC
Q 022009 228 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADR--TQTIEQAGLAN-SVVIQKF 304 (304)
Q Consensus 228 ~p~t~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~--s~TL~eagL~n-a~ivqk~ 304 (304)
++.|+||||||||+|++++|+.++||++||+||.........+|.|++ +||+|.|++. ++||+|+||++ ++|+++|
T Consensus 2 ~~~~~I~iRlPdG~ri~~~F~~~~tl~~v~~~v~~~~~~~~~~f~L~t-~~Prk~l~~~d~~~tL~e~gL~p~~~l~v~~ 80 (80)
T smart00166 2 SDQCRLQIRLPDGSRLVRRFPSSDTLRTVYEFVSAALTDGNDPFTLNS-PFPRRTFTKDDYSKTLLELALLPSSTLVLEP 80 (80)
T ss_pred CCeEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHcccCCCCCEEEEe-CCCCcCCccccccCCHHHCCCCCceEEEEeC
Confidence 478999999999999999999999999999999765544467899998 9999999854 79999999995 8888887
No 7
>cd01773 Faf1_like1_UBX Faf1 ike-1 UBX domain. Faf1_like1 is a protein of unknown function with a domain architecture that includes the UAS (ubiquitin-associated) and UBX (ubiquitin-like) domains. This protein is related to other UBA/UBX-containing proteins like Faf1, p47, and SAKS1 and may serve as an adaptor molecule that shuttles proteins to the proteasome for degradation. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=99.79 E-value=7.2e-19 Score=136.68 Aligned_cols=73 Identities=22% Similarity=0.373 Sum_probs=65.0
Q ss_pred CCCceeEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCcccc--CCCCchhhhCCCC-eeEE
Q 022009 227 NLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA--DRTQTIEQAGLAN-SVVI 301 (304)
Q Consensus 227 ~~p~t~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~--d~s~TL~eagL~n-a~iv 301 (304)
++|+|+||||||||+|+++||+.++||.+||.||.+. .....+|.|++ +||+|.|+ |.++||+||||++ ++|+
T Consensus 2 ~~~~t~i~vRlP~G~r~~rrF~~~~~L~~v~~fv~~~-g~~~~~f~L~t-~FPRr~~~~~d~~~TL~e~GL~P~~~Lf 77 (82)
T cd01773 2 NGPKARLMLRYPDGKREQIALPEQAKLLALVRHVQSK-GYPNERFELLT-NFPRRKLSHLDYDITLQEAGLCPQETVF 77 (82)
T ss_pred CCCeeEEEEECCCCCEEEEEeCCCCcHHHHHHHHHhc-CCCCCCEEEec-CCCCcccCCcccCCCHHHcCCCCCcEEE
Confidence 6899999999999999999999999999999999984 34478999997 99999998 5579999999998 4443
No 8
>cd01774 Faf1_like2_UBX Faf1 ike-2 UBX domain. Faf1_like2 is a protein of unknown function with a domain architecture that includes the UAS (ubiquitin-associated) and UBX (ubiquitin-like) domains. This protein is related to other UBA/UBX-containing proteins like Faf1, p47, and SAKS1 and may serve as an adaptor molecule that shuttles proteins to the proteasome for degradation. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=99.77 E-value=1.2e-18 Score=136.51 Aligned_cols=69 Identities=29% Similarity=0.505 Sum_probs=61.3
Q ss_pred CCceeEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCcccc-------CCCCchhhhCCCCe
Q 022009 228 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA-------DRTQTIEQAGLANS 298 (304)
Q Consensus 228 ~p~t~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~-------d~s~TL~eagL~na 298 (304)
...|+||||||||+|+++||+.+|||++||+||.+ .+....+|.|++ +||+|.|+ |.++||+||||.|+
T Consensus 2 ~~~~~I~iRlp~G~Rl~rrF~~~~tl~~l~~fv~~-~~~~~~~f~L~t-~FPrr~~~~~~~~~~~~~~TL~eaGL~~s 77 (85)
T cd01774 2 PDTVKIVFKLPNGTRVERRFLFTQSLRVIHDFLFS-LKETPEKFQIVT-NFPRRVLPCLPSEGDPPPPTLLEAGLSNS 77 (85)
T ss_pred CceEEEEEECCCCCEEEEEeCCCCcHHHHHHHHHh-CCCCCCcEEEec-CCCCccccccccccCcCCCCHHHcCCCCc
Confidence 35799999999999999999999999999999964 445567999997 99999997 45889999999984
No 9
>cd01771 Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated factor1) is a nucleolar protein that was first identified as an interaction partner of the death receptor Fas. Faf1 contains N-terminal UAS (ubiquitin-associated) and C-terminal UBX (ubiquitin-like) domains and is closely related to other UBA/UBX-containing proteins like p47, Rep8 and SAKS1. Faf1 is thought to be involved in 18S rRNA synthesis and/or 40S ribosomal subunit assembly. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=99.77 E-value=2.1e-18 Score=133.76 Aligned_cols=73 Identities=19% Similarity=0.297 Sum_probs=64.1
Q ss_pred CCCceeEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCcccc--CCCCchhhhCCCC-eeEE
Q 022009 227 NLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA--DRTQTIEQAGLAN-SVVI 301 (304)
Q Consensus 227 ~~p~t~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~--d~s~TL~eagL~n-a~iv 301 (304)
++|+|+||||||||+|+++||+.++||++||+||.+... ...+|.|++ +||+|+|+ |.+.||+|+||.+ ++|+
T Consensus 1 ~~~~~~i~iRlP~G~r~~rrF~~t~~L~~l~~fv~~~~~-~~~~f~L~t-~fPRk~~~~~d~~~TL~e~gL~p~~~L~ 76 (80)
T cd01771 1 GEPISKLRVRTPSGDFLERRFLGDTPLQVLLNFVASKGY-PIDEYKLLS-SWPRRDLTQLDPNFTLLELKLYPQETLI 76 (80)
T ss_pred CCCeEEEEEECCCCCEEEEEeCCCCcHHHHHHHHHhcCC-CCCCEEEec-CCCCCCCcCCCCCCcHHHcCCCCCcEEE
Confidence 478999999999999999999999999999999987532 257999997 99999997 6678999999997 4444
No 10
>cd01772 SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-substrate-1), also known as Y33K, is a widely expressed protein containing N-terminal UBA (ubiquitin-associated) and C-terminal UBX (ubiqiutin-like) domains that was identified as a substrate of stress-activated protein kinases (SAPKs). SAKS1 is related evolutionarily to two other UBA/UBX-containing proteins, p47 and Faf1. The UBA and UBX domains of SAKS1 bind ubiquitin tetramers and valosin-containing protein (VCP), respectively suggesting a role for SAKS1 as an adaptor that directs VCP to polyubiquitinated proteins facilitating its destruction by the proteasome. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=99.75 E-value=6.3e-18 Score=130.52 Aligned_cols=73 Identities=29% Similarity=0.540 Sum_probs=63.2
Q ss_pred CceeEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCcccc--CCCCchhhhCCCC-eeE-Eee
Q 022009 229 PSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA--DRTQTIEQAGLAN-SVV-IQK 303 (304)
Q Consensus 229 p~t~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~--d~s~TL~eagL~n-a~i-vqk 303 (304)
..|+||||||||+|++++|+.++||.+||+||..+... ..+|.|++ +||+|.|+ |.++||+||||.| |+| |||
T Consensus 3 ~~~~i~iRlp~G~~~~~~F~~~~tl~~v~~fV~~~~~~-~~~f~L~t-~fPrk~~~~~d~~~TL~elgL~Psa~L~v~~ 79 (79)
T cd01772 3 TETRIQIRLLDGTTLKQTFKAREQLAAVRLFVELNTGN-GGPFTLMT-PFPRKVFTEDDMEKPLQELGLVPSAVLIVTK 79 (79)
T ss_pred cEEEEEEECCCCCEEEEEeCCCChHHHHHHHHHHcCCC-CCCEEEEe-CCCCeECCcccccCCHHHCCCCCceEEEEeC
Confidence 46899999999999999999999999999999987543 47899997 99999998 4589999999998 444 443
No 11
>PF00789 UBX: UBX domain; InterPro: IPR001012 The UBX domain is found in ubiquitin-regulatory proteins, which are members of the ubiquitination pathway, as well as a number of other proteins including FAF-1 (FAS-associated factor 1), the human Rep-8 reproduction protein and several hypothetical proteins from yeast. The function of the UBX domain is not known although the fragment of avian FAF-1 containing the UBX domain causes apoptosis of transfected cells.; GO: 0005515 protein binding; PDB: 3QX1_A 1H8C_A 3QCA_B 3QQ8_B 3QC8_B 3R3M_A 3QWZ_B 1S3S_H 1JRU_A 1I42_A ....
Probab=99.74 E-value=4.4e-18 Score=131.27 Aligned_cols=78 Identities=29% Similarity=0.525 Sum_probs=67.8
Q ss_pred CCCCceeEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCC-eEEEecCCCCccccCCC-CchhhhCCCC-eeEEe
Q 022009 226 ENLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARN-YQLQMMGFPPKVLADRT-QTIEQAGLAN-SVVIQ 302 (304)
Q Consensus 226 ~~~p~t~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~-f~L~t~~fP~k~l~d~s-~TL~eagL~n-a~ivq 302 (304)
+..+.|+||||||||++++++|+.++||++||+||.........+ |.|++ +||++.|++.+ +||+||||.+ ++|++
T Consensus 2 ~~~~~~~I~vRlpdG~~l~~~F~~~~tl~~l~~~v~~~~~~~~~~~f~L~~-~~Pr~~l~~~~~~tl~e~~l~p~~~l~v 80 (82)
T PF00789_consen 2 EESDVVRIQVRLPDGSRLQRRFPKSDTLQDLYDFVESQLFSPEESDFELIT-AFPRRELTDEDSKTLEEAGLLPSATLIV 80 (82)
T ss_dssp STSSEEEEEEEETTSTEEEEEEETTSBHHHHHHHHHHHHHCTTTSSEEEEE-SSSTEECCSTTTSBTCCCTTSSCEEEEE
T ss_pred CCCCEEEEEEECCCCCEEEEEECCcchHHHHHHHHHHhcCCCCCccEEEEe-CCCCcCCCccccccHHHhcCCCCeEEEE
Confidence 456789999999999999999999999999999999876554443 99997 99999999665 9999999996 88888
Q ss_pred eC
Q 022009 303 KF 304 (304)
Q Consensus 303 k~ 304 (304)
+|
T Consensus 81 ~~ 82 (82)
T PF00789_consen 81 EK 82 (82)
T ss_dssp E-
T ss_pred EC
Confidence 87
No 12
>KOG2689 consensus Predicted ubiquitin regulatory protein [Posttranslational modification, protein turnover, chaperones]
Probab=99.41 E-value=8.8e-13 Score=121.85 Aligned_cols=77 Identities=26% Similarity=0.496 Sum_probs=69.2
Q ss_pred CCCceeEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCcccc--CCCCchhhhCCCC-eeEEee
Q 022009 227 NLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA--DRTQTIEQAGLAN-SVVIQK 303 (304)
Q Consensus 227 ~~p~t~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~--d~s~TL~eagL~n-a~ivqk 303 (304)
....|+|||||+||+.+..+||...|+.+||.||+.++.+...+|.|++ +||++.|+ |+.++|++++|++ |+|+.+
T Consensus 207 ~ys~crlQiRl~DG~Tl~~tF~a~E~L~~VR~wVd~n~~~~~~P~~f~t-~fPR~tf~edD~~KpLq~L~L~Psa~lil~ 285 (290)
T KOG2689|consen 207 DYSQCRLQIRLPDGQTLTQTFNARETLAAVRLWVDLNRGDGLDPYSFHT-GFPRVTFTEDDELKPLQELDLVPSAVLILE 285 (290)
T ss_pred cccceEEEEEcCCCCeeeeecCchhhHHHHHHHHHHhccCCCCCeeeec-CCCceecccccccccHHHhccccchheecc
Confidence 4568999999999999999999999999999999999887778999997 99999997 5678999999998 666654
Q ss_pred C
Q 022009 304 F 304 (304)
Q Consensus 304 ~ 304 (304)
|
T Consensus 286 ~ 286 (290)
T KOG2689|consen 286 P 286 (290)
T ss_pred c
Confidence 3
No 13
>KOG1364 consensus Predicted ubiquitin regulatory protein, contains UAS and UBX domains [Posttranslational modification, protein turnover, chaperones]
Probab=98.98 E-value=3.1e-10 Score=108.29 Aligned_cols=74 Identities=27% Similarity=0.429 Sum_probs=63.9
Q ss_pred ceeEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCC-CCCeEEEecCCCCcccc--CCCCchhhhCCCCe--eEEeeC
Q 022009 230 STSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGT-ARNYQLQMMGFPPKVLA--DRTQTIEQAGLANS--VVIQKF 304 (304)
Q Consensus 230 ~t~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~-~~~f~L~t~~fP~k~l~--d~s~TL~eagL~na--~ivqk~ 304 (304)
+|+|+||+|||+|.++||..++||+-||.|+..+..+. ...|.|+. +||++.+. +.+.||++|||+|+ ++.+-|
T Consensus 277 vt~i~vR~pdG~R~qrkf~~sepv~ll~~~~~s~~dg~~k~~FkLv~-a~P~~k~l~~~~daT~~eaGL~nS~~~~~~e~ 355 (356)
T KOG1364|consen 277 VTSIQVRFPDGRRKQRKFLKSEPVQLLWSFCYSHMDGSDKKRFKLVQ-AIPASKTLDYGADATFKEAGLANSETLLSVEW 355 (356)
T ss_pred eeEEEEecCCccHHHHhhccccHHHHHHHHHHHhhcccccccceeee-cccchhhhhccccchHHHhccCcccccccccc
Confidence 67899999999999999999999999999999887666 78899997 99987765 35789999999997 554433
No 14
>KOG2507 consensus Ubiquitin regulatory protein UBXD2, contains UAS and UBX domains [General function prediction only]
Probab=98.88 E-value=1.5e-09 Score=105.81 Aligned_cols=69 Identities=17% Similarity=0.339 Sum_probs=62.9
Q ss_pred CCceeEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCcccc--CCCCchhhhCCCC
Q 022009 228 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA--DRTQTIEQAGLAN 297 (304)
Q Consensus 228 ~p~t~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~--d~s~TL~eagL~n 297 (304)
-..|+||||||||+.++-+|..++-+..|++||..........|.|.+ .||+|+|+ |..+||.|+.|.+
T Consensus 312 ~d~~rLqiRLPdGssfte~Fps~~vL~~vr~yvrq~~~i~~g~f~Lat-pyPRReft~eDy~KtllEl~L~p 382 (506)
T KOG2507|consen 312 ADDVRLQIRLPDGSSFTEKFPSTSVLRMVRDYVRQNQTIGLGAFDLAT-PYPRREFTDEDYDKTLLELRLFP 382 (506)
T ss_pred cceeEEEEecCCccchhhcCCcchHHHHHHHHHHhcccccccceeecc-ccccccccchhhhhhHHHhccCC
Confidence 467999999999999999999999999999999977655588999997 99999998 4578999999997
No 15
>KOG1363 consensus Predicted regulator of the ubiquitin pathway (contains UAS and UBX domains) [Signal transduction mechanisms]
Probab=98.39 E-value=5.5e-07 Score=90.23 Aligned_cols=74 Identities=24% Similarity=0.453 Sum_probs=63.9
Q ss_pred CCCceeEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccC--CCCchhhhCCCC--eeEEe
Q 022009 227 NLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLAD--RTQTIEQAGLAN--SVVIQ 302 (304)
Q Consensus 227 ~~p~t~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d--~s~TL~eagL~n--a~ivq 302 (304)
..++++|.||+|+|+|+.+||..++++++||+||..+. .....|.|.+ +||++.+.+ .+.||++.||.+ .+|++
T Consensus 380 ~~~~~~l~iR~P~G~r~~RrF~~s~~~q~l~~~v~~~~-~~~~e~~~~~-~fPr~~~~~~~~~~sl~~~~l~p~qe~lfl 457 (460)
T KOG1363|consen 380 EEEAITVAIRLPSGTRLERRFLKSDKLQILYDYVDSNG-FHPEEYSLNT-SFPRRPLGDYEHSSSLQDIGLTPRQETLFL 457 (460)
T ss_pred cccceeeEEECCCCCeeeeeeecccchhHHHHHHHhcc-CCchhhcccc-CCCcccccccccccccccCCcccccceeee
Confidence 45688999999999999999999999999999999875 4467899987 899999985 478999999997 44444
No 16
>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain. DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.
Probab=97.34 E-value=0.00081 Score=50.53 Aligned_cols=68 Identities=15% Similarity=0.252 Sum_probs=54.7
Q ss_pred EEEEcC-CCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC-eeEEee
Q 022009 233 VQIRLA-DGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVIQK 303 (304)
Q Consensus 233 IqIRl~-dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~ivqk 303 (304)
|-||+. +|+.+.+....+.||++|...|.....-......|+ |=.|.|.|++.||+++|+.+ ++|+.+
T Consensus 1 l~v~~~~~g~~~~l~v~~~~TV~~lK~~I~~~~gip~~~q~Li---~~Gk~L~D~~~~L~~~gi~~~~~l~l~ 70 (71)
T cd01796 1 ITVYTARSETTFSLDVDPDLELENFKALCEAESGIPASQQQLI---YNGRELVDNKRLLALYGVKDGDLVVLR 70 (71)
T ss_pred CEEEECCCCCEEEEEECCcCCHHHHHHHHHHHhCCCHHHeEEE---ECCeEccCCcccHHHcCCCCCCEEEEe
Confidence 468999 999999999999999999999987643224445663 67899998878999999996 776654
No 17
>cd01807 GDX_N ubiquitin-like domain of GDX. GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.
Probab=97.15 E-value=0.0022 Score=48.27 Aligned_cols=66 Identities=14% Similarity=0.239 Sum_probs=53.7
Q ss_pred eEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC-eeEE
Q 022009 232 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI 301 (304)
Q Consensus 232 ~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~iv 301 (304)
+|.||..+|+.+.+.+..++||++|++-|.....-....+.|+ |=.+.|.|. .||.+.|+.+ ++|.
T Consensus 2 ~i~vk~~~G~~~~l~v~~~~tV~~lK~~i~~~~gi~~~~q~L~---~~G~~L~d~-~~L~~~~i~~~~~l~ 68 (74)
T cd01807 2 FLTVKLLQGRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLL---FKGKALADD-KRLSDYSIGPNAKLN 68 (74)
T ss_pred EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEE---ECCEECCCC-CCHHHCCCCCCCEEE
Confidence 5889999999999999999999999999987642224556774 678999874 8999999996 5553
No 18
>cd01806 Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.
Probab=97.10 E-value=0.003 Score=47.03 Aligned_cols=65 Identities=14% Similarity=0.243 Sum_probs=52.0
Q ss_pred eEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC-eeE
Q 022009 232 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV 300 (304)
Q Consensus 232 ~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~i 300 (304)
+|.||..+|+.+.+++..+.||++|.+.|.....-......|+ |-.+.|.| +.||.+.++.+ ++|
T Consensus 2 ~i~v~~~~g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~---~~g~~L~d-~~tl~~~~i~~g~~i 67 (76)
T cd01806 2 LIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLI---YSGKQMND-DKTAADYKLEGGSVL 67 (76)
T ss_pred EEEEEeCCCCEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEE---ECCeEccC-CCCHHHcCCCCCCEE
Confidence 5889999999999999999999999999987642223445553 67888876 58999999996 444
No 19
>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein. DC_UbP (dendritic cell derived ubiquitin-like protein) is a ubiquitin-like protein from human dendritic cells that is expressed in the mitochondrion. The ubiquitin-like domain of this protein is found at the C-terminus and lacks the canonical gly-gly motif of ubiquitin required for ubiquitinization. DC_UbP is expressed in tumor cells but not in normal human adult tissue suggesting a role for DC_UbP in tumorogenesis.
Probab=97.09 E-value=0.0018 Score=48.68 Aligned_cols=65 Identities=15% Similarity=0.305 Sum_probs=50.8
Q ss_pred EEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCCeeEE
Q 022009 233 VQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLANSVVI 301 (304)
Q Consensus 233 IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~na~iv 301 (304)
|.||+.+|+.+...+..++||++|++.|.....-......|+ |=-+.|.| +.||.++++.+..+|
T Consensus 1 ~~vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~Li---~~G~~L~D-~~~l~~~~i~~~~tv 65 (70)
T cd01794 1 LKVRLSTGKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWF---FSGKLLTD-KTRLQETKIQKDYVV 65 (70)
T ss_pred CeEEcCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEE---ECCeECCC-CCCHHHcCCCCCCEE
Confidence 468999999999999999999999999987532223344553 77888988 589999999974333
No 20
>cd01792 ISG15_repeat1 ISG15 ubiquitin-like protein, first repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains that becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=97.00 E-value=0.0046 Score=47.34 Aligned_cols=68 Identities=19% Similarity=0.222 Sum_probs=54.5
Q ss_pred eeEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC-eeE
Q 022009 231 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV 300 (304)
Q Consensus 231 t~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~i 300 (304)
..|.||..+|+.+...+..+.||++|.+-|.....-......|.. -|..+.|.|+ .||.+.|+.+ ++|
T Consensus 3 ~~i~Vk~~~G~~~~~~v~~~~TV~~lK~~I~~~~~i~~~~qrL~~-~~~G~~L~D~-~tL~~~gi~~gs~l 71 (80)
T cd01792 3 WDLKVKMLGGNEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLAH-LDSREVLQDG-VPLVSQGLGPGSTV 71 (80)
T ss_pred eEEEEEeCCCCEEEEEcCCCCcHHHHHHHHHHHhCCCHHHEEEEe-ccCCCCCCCC-CCHHHcCCCCCCEE
Confidence 478999999999999999999999999999876432345667743 4777888874 7999999986 444
No 21
>cd01804 midnolin_N Ubiquitin-like domain of midnolin. midnolin_N Midnolin (midbrain nucleolar protein) is expressed in the nucleolus and is thought to regulate genes involved in neurogenesis. Midnolin contains an amino-terminal ubiquitin-like domain.
Probab=96.95 E-value=0.0045 Score=47.36 Aligned_cols=65 Identities=17% Similarity=0.203 Sum_probs=51.3
Q ss_pred eEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC-eeEE
Q 022009 232 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI 301 (304)
Q Consensus 232 ~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~iv 301 (304)
+|.||...|+.....+..+.||++|++-|.....-......| .|..+.|.|. ||+++|+.+ ++|+
T Consensus 3 ~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~~~~~~~qrL---~~~Gk~L~d~--~L~~~gi~~~~~i~ 68 (78)
T cd01804 3 NLNIHSTTGTRFDLSVPPDETVEGLKKRISQRLKVPKERLAL---LHRETRLSSG--KLQDLGLGDGSKLT 68 (78)
T ss_pred EEEEEECCCCEEEEEECCcCHHHHHHHHHHHHhCCChHHEEE---EECCcCCCCC--cHHHcCCCCCCEEE
Confidence 688999999999999999999999999998764222233444 4788999885 899999985 5554
No 22
>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....
Probab=96.82 E-value=0.0038 Score=45.85 Aligned_cols=62 Identities=16% Similarity=0.263 Sum_probs=50.3
Q ss_pred EcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC-eeEE
Q 022009 236 RLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI 301 (304)
Q Consensus 236 Rl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~iv 301 (304)
|..+|+.+...++.++||.+|.+.|.....-......|+ |-.+.|. ++.||.+.|+.+ ++|+
T Consensus 1 k~~~g~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~---~~G~~L~-d~~tL~~~~i~~~~~I~ 63 (69)
T PF00240_consen 1 KTLSGKTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLI---YNGKELD-DDKTLSDYGIKDGSTIH 63 (69)
T ss_dssp EETTSEEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEE---ETTEEES-TTSBTGGGTTSTTEEEE
T ss_pred CCCCCcEEEEEECCCCCHHHhhhhcccccccccccceee---eeeeccc-CcCcHHHcCCCCCCEEE
Confidence 567899999999999999999999998754334556663 7889995 479999999996 6554
No 23
>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein. Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules.
Probab=96.80 E-value=0.0071 Score=44.53 Aligned_cols=66 Identities=14% Similarity=0.206 Sum_probs=51.9
Q ss_pred eEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC-eeEE
Q 022009 232 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI 301 (304)
Q Consensus 232 ~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~iv 301 (304)
+|-||..+|+....++..++||++|.+-|.....-......|+ |..+.|.| +.||.+.|+.+ +.|.
T Consensus 2 ~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~---~~g~~L~d-~~~L~~~~i~~~~~l~ 68 (72)
T cd01809 2 EIKVKTLDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLI---YSGRVLKD-DETLSEYKVEDGHTIH 68 (72)
T ss_pred EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEE---ECCEECCC-cCcHHHCCCCCCCEEE
Confidence 5889999999999999999999999999987643223344553 56788877 58999999986 5543
No 24
>cd01791 Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.
Probab=96.72 E-value=0.013 Score=44.53 Aligned_cols=67 Identities=15% Similarity=0.115 Sum_probs=52.1
Q ss_pred eeEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC-eeEE
Q 022009 231 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI 301 (304)
Q Consensus 231 t~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~iv 301 (304)
.+|.||-..|+.+...+..+.||++|.+-|.....-....-.| .|..+.|.| +.||++.||.+ ++|.
T Consensus 2 ~~i~vkt~~Gk~~~~~v~~~~TV~~LK~~I~~~~~~~~~~qrL---i~~Gk~L~D-~~tL~~ygi~~~stv~ 69 (73)
T cd01791 2 IEVVCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVL---KKWYTIFKD-HISLGDYEIHDGMNLE 69 (73)
T ss_pred EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEE---EeCCcCCCC-CCCHHHcCCCCCCEEE
Confidence 4688899999999999999999999999998764222223334 477888887 47999999986 5554
No 25
>cd01805 RAD23_N Ubiquitin-like domain of RAD23. RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL).
Probab=96.67 E-value=0.011 Score=44.44 Aligned_cols=66 Identities=14% Similarity=0.286 Sum_probs=51.8
Q ss_pred eEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCC--CCCCeEEEecCCCCccccCCCCchhhhCCCC-eeEE
Q 022009 232 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPG--TARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI 301 (304)
Q Consensus 232 ~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~--~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~iv 301 (304)
.|.||..+|+...+.+..++||.+|++.|.....- ......| .|..+.|.| +.||.++|+.+ ++|+
T Consensus 2 ~i~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L---~~~G~~L~d-~~~L~~~~i~~~~~i~ 70 (77)
T cd01805 2 KITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKL---IYSGKILKD-DTTLEEYKIDEKDFVV 70 (77)
T ss_pred EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEE---EECCEEccC-CCCHHHcCCCCCCEEE
Confidence 57899999999999999999999999999875432 2233445 378899987 48999999996 4443
No 26
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=96.58 E-value=0.011 Score=44.03 Aligned_cols=65 Identities=17% Similarity=0.265 Sum_probs=51.3
Q ss_pred eEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC-eeE
Q 022009 232 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV 300 (304)
Q Consensus 232 ~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~i 300 (304)
.|-||..+|+.+...+..++||++|.+.|.....-......|. |..+.|.| +.||.+.|+.+ ++|
T Consensus 2 ~i~v~~~~g~~~~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~---~~g~~L~d-~~~L~~~~i~~~~~i 67 (76)
T cd01803 2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI---FAGKQLED-GRTLSDYNIQKESTL 67 (76)
T ss_pred EEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCHHHeEEE---ECCEECCC-CCcHHHcCCCCCCEE
Confidence 4789999999999999999999999999987642223344553 67888887 47999999986 444
No 27
>PF12090 Spt20: Spt20 family; InterPro: IPR021950 This presumed domain is found in the Spt20 proteins from both human and yeast. The Spt20 protein is part of the SAGA complex which is a large cmplex mediating histone deacetylation. Yeast Spt20 has been shown to play a role in structural integrity of the SAGA complex as as no intact SAGA could be purified in spt20 deletion strains.
Probab=96.58 E-value=0.0022 Score=57.12 Aligned_cols=58 Identities=19% Similarity=0.222 Sum_probs=48.2
Q ss_pred ceEEEEEeccceee----cCCCCccCCChhhHHHHHHHHcCCCCccccCCC-------CCCceEEEEeec
Q 022009 116 IVHNIVFWANGFTV----NDGPLRRLDDPENASFLESIKKSECPKELEPAD-------KRSSVHVNLIRR 174 (304)
Q Consensus 116 v~~~It~w~nGF~V----dDGpfR~yddP~n~~FL~~I~~G~~P~EL~~~~-------~~~~V~v~v~~r 174 (304)
...+|+||-++|.+ .+.-..+|++|. +.||+.|.+|.+|..|+... .++-|-|+|.|+
T Consensus 14 pSl~vhL~p~~f~f~~~~~~~~~~pY~~~~-k~~L~~I~~~~iP~~Lle~l~~~~v~FYdGClIveV~D~ 82 (182)
T PF12090_consen 14 PSLIVHLYPNHFRFSLNDQQDGSFPYNSPM-KEFLEYIDAGEIPHDLLELLDDANVPFYDGCLIVEVRDH 82 (182)
T ss_pred CeEEEEECCCCeeEeecCCCCceecCCchH-HHHHHHHHcCCCCHHHHHHHHhCCCeeEcCEEEEEEecc
Confidence 46889999999999 577789999999 99999999999999888654 344567777753
No 28
>PTZ00044 ubiquitin; Provisional
Probab=96.56 E-value=0.011 Score=44.34 Aligned_cols=65 Identities=12% Similarity=0.252 Sum_probs=52.3
Q ss_pred eEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC-eeE
Q 022009 232 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV 300 (304)
Q Consensus 232 ~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~i 300 (304)
.|-||..+|+.+..++..+.||.+|..-|.....-......|. |-.+.|.| +.||.+.++.+ +.|
T Consensus 2 ~i~vk~~~G~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~---~~g~~L~d-~~~l~~~~i~~~~~i 67 (76)
T PTZ00044 2 QILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLI---YSGKQMSD-DLKLSDYKVVPGSTI 67 (76)
T ss_pred EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEE---ECCEEccC-CCcHHHcCCCCCCEE
Confidence 4789999999999999999999999999988643224455663 77889986 57899999996 444
No 29
>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein. parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.
Probab=96.56 E-value=0.0094 Score=44.25 Aligned_cols=64 Identities=17% Similarity=0.308 Sum_probs=51.7
Q ss_pred EEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC-eeE
Q 022009 233 VQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV 300 (304)
Q Consensus 233 IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~i 300 (304)
|-||..+|..+...+..++||++|.+.|.....-......|+ |=.+.|.|. .||.++|+.+ ++|
T Consensus 1 i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~q~Li---~~G~~L~d~-~~l~~~~i~~~stl 65 (70)
T cd01798 1 VYVRTNTGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVI---FAGKELRNT-TTIQECDLGQQSIL 65 (70)
T ss_pred CEEEcCCCCEEEEEECCCChHHHHHHHHHHHHCCCHHHeEEE---ECCeECCCC-CcHHHcCCCCCCEE
Confidence 458999999999999999999999999987643224456663 778999874 8999999996 555
No 30
>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and ATGP4 are plant-specific isoprenylated GTP-binding proteins with a single fold that resembles ubiquitin. The function of these proteins is unknown.
Probab=96.48 E-value=0.0064 Score=50.12 Aligned_cols=62 Identities=16% Similarity=0.302 Sum_probs=49.0
Q ss_pred CceeEEEEcCCCCEE-EEecCCCCCHHHHHHHHHhhCCCC-------CCCeEEEecCCCCccccCCCCchhhhC
Q 022009 229 PSTSVQIRLADGTRL-IAHFNLHHTISDIHSFIDASRPGT-------ARNYQLQMMGFPPKVLADRTQTIEQAG 294 (304)
Q Consensus 229 p~t~IqIRl~dG~rl-~~rFn~s~TV~dvr~fv~~~~~~~-------~~~f~L~t~~fP~k~l~d~s~TL~eag 294 (304)
....|++||+||+-+ -.+|..++||.+|.+-|....+.. ...-.|+ |--|.|.| +.||++++
T Consensus 3 ~~~e~kfrl~dg~digp~~~~~sdTV~~lKekI~~~~p~~ke~~P~~~~~qKLI---ysGKiLeD-~~TL~d~~ 72 (113)
T cd01814 3 EQIEIKFRLYDGSDIGPKRYPAATTVDFLKERVVSQWPKDKEVGPKTVNEVKLI---SAGKILEN-SKTVGECR 72 (113)
T ss_pred ccEEEEEEccCCCccCccccChhhHHHHHHHHHHHhcccccccCCCCHHHeEEE---eCCeecCC-CCcHHHhC
Confidence 456799999999876 789999999999999999777531 1122332 67888887 58999999
No 31
>cd01810 ISG15_repeat2 ISG15 ubiquitin-like protein, second repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains and becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=96.47 E-value=0.011 Score=44.42 Aligned_cols=64 Identities=19% Similarity=0.336 Sum_probs=51.8
Q ss_pred EEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC-eeE
Q 022009 233 VQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV 300 (304)
Q Consensus 233 IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~i 300 (304)
|-||.++|+.+...+..++||.+|++-|.....-....+.|. |=.+.|.|+ .||.+.|+.+ ++|
T Consensus 1 i~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~q~L~---~~G~~L~D~-~tL~~~~i~~~~tl 65 (74)
T cd01810 1 ILVRNDKGRSSIYEVQLTQTVATLKQQVSQRERVQADQFWLS---FEGRPMEDE-HPLGEYGLKPGCTV 65 (74)
T ss_pred CEEECCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEE---ECCEECCCC-CCHHHcCCCCCCEE
Confidence 468999999999999999999999999986543224557774 678999975 8999999986 444
No 32
>cd01808 hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC2. hPLIC-1 and hPLIC-2 (human homologs of the yeast ubiquitin-like Dsk2 protein) are type2 UBL's (ubiquitin-like) proteins that are thought to serve as adaptors that link the ubiquitination machinery to the proteasome. The hPLIC's have an N-terminal UBL domain that binds the S5a subunit of the proteasome and a C-terminal UBA (ubiquitin-associated) domain that binds a ubiquitylated protein.
Probab=96.35 E-value=0.018 Score=42.82 Aligned_cols=66 Identities=15% Similarity=0.201 Sum_probs=51.3
Q ss_pred eEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC-eeEEe
Q 022009 232 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVIQ 302 (304)
Q Consensus 232 ~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~ivq 302 (304)
+|-||..+|. ....+..+.||++|++-|.....-....+.| -|..+.|.|. .||.++|+.+ ++|.+
T Consensus 2 ~i~vk~~~g~-~~l~v~~~~TV~~lK~~I~~~~~i~~~~~~L---i~~Gk~L~d~-~tL~~~~i~~~stl~l 68 (71)
T cd01808 2 KVTVKTPKDK-EEIEIAEDASVKDFKEAVSKKFKANQEQLVL---IFAGKILKDT-DTLTQHNIKDGLTVHL 68 (71)
T ss_pred EEEEEcCCCC-EEEEECCCChHHHHHHHHHHHhCCCHHHEEE---EECCeEcCCC-CcHHHcCCCCCCEEEE
Confidence 5889999996 4788899999999999998764322445666 3788999874 7999999985 66643
No 33
>PF11543 UN_NPL4: Nuclear pore localisation protein NPL4; InterPro: IPR024682 Npl4, along with Ufd1, forms the heterodimer adaptor complex UN, which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway. Npl4 has a N-terminal ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert []. This entry represents the ubiquitin-like domain.; PDB: 2PJH_A 1WF9_A.
Probab=96.24 E-value=0.0063 Score=47.16 Aligned_cols=66 Identities=20% Similarity=0.263 Sum_probs=39.1
Q ss_pred eeEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCC-ccc-cCCCCchhhhCCCCe
Q 022009 231 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPP-KVL-ADRTQTIEQAGLANS 298 (304)
Q Consensus 231 t~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~-k~l-~d~s~TL~eagL~na 298 (304)
--||||.+||...+ .+..++||.+|++-|..........|.|.. .... ..+ .+.++||.++||.+.
T Consensus 5 milRvrS~dG~~Ri-e~~~~~t~~~L~~kI~~~l~~~~~~~~L~~-~~~~~~~l~s~~~~tl~~lglkHG 72 (80)
T PF11543_consen 5 MILRVRSKDGMKRI-EVSPSSTLSDLKEKISEQLSIPDSSQSLSK-DRNNKEELKSSDSKTLSSLGLKHG 72 (80)
T ss_dssp -EEEEE-SSEEEEE-EE-TTSBHHHHHHHHHHHS---TTT---BS-SGGGGGCSSS-TT-CCCCT---TT
T ss_pred EEEEEECCCCCEEE-EcCCcccHHHHHHHHHHHcCCCCcceEEEe-cCCCCcccccCCcCCHHHcCCCCc
Confidence 35899999997433 467899999999999987655456788864 4333 344 256899999999973
No 34
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=96.16 E-value=0.022 Score=40.52 Aligned_cols=61 Identities=16% Similarity=0.259 Sum_probs=47.7
Q ss_pred eEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC
Q 022009 232 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN 297 (304)
Q Consensus 232 ~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n 297 (304)
.|.||..+ .....++..+.||++|...|.....-......|+ |-.+.|.| +.||.++|+.+
T Consensus 2 ~i~vk~~~-~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~---~~g~~L~d-~~tL~~~~i~~ 62 (64)
T smart00213 2 ELTVKTLD-GTITLEVKPSDTVSELKEKIAELTGIPVEQQRLI---YKGKVLED-DRTLADYNIQD 62 (64)
T ss_pred EEEEEECC-ceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEE---ECCEECCC-CCCHHHcCCcC
Confidence 58899999 6788999999999999999987543223335553 56788887 48999999875
No 35
>cd01812 BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).
Probab=96.01 E-value=0.037 Score=40.65 Aligned_cols=65 Identities=20% Similarity=0.326 Sum_probs=50.1
Q ss_pred eEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC-eeEE
Q 022009 232 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI 301 (304)
Q Consensus 232 ~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~iv 301 (304)
+|.||.. |....+++..+.||.+|.+-|.....-......|. |-.+.|.| +.||.++|+.+ ++|+
T Consensus 2 ~i~vk~~-g~~~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~---~~g~~l~d-~~~L~~~~i~~g~~l~ 67 (71)
T cd01812 2 RVRVKHG-GESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLI---FKGKERDD-AETLDMSGVKDGSKVM 67 (71)
T ss_pred EEEEEEC-CEEEEEEECCCCcHHHHHHHHHHhhCCChHHeEEe---eCCcccCc-cCcHHHcCCCCCCEEE
Confidence 6788886 88888999999999999999987643224456664 55788876 58999999986 5544
No 36
>PF13881 Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB: 1SE9_A 1WGH_A 2GOW_A.
Probab=95.88 E-value=0.031 Score=46.00 Aligned_cols=63 Identities=25% Similarity=0.407 Sum_probs=46.1
Q ss_pred ceeEEEEcCCCC-EEEEecCCCCCHHHHHHHHHhhCCCC-------CCCeEEEecCCCCccccCCCCchhhhCCC
Q 022009 230 STSVQIRLADGT-RLIAHFNLHHTISDIHSFIDASRPGT-------ARNYQLQMMGFPPKVLADRTQTIEQAGLA 296 (304)
Q Consensus 230 ~t~IqIRl~dG~-rl~~rFn~s~TV~dvr~fv~~~~~~~-------~~~f~L~t~~fP~k~l~d~s~TL~eagL~ 296 (304)
...|++||.||+ +...+|..+.||++|.++|...-|.. .....|+ |=-|.|.| +.||.++.+.
T Consensus 2 ~i~lkf~l~~G~d~~~~~~~~~~TV~~lKe~i~~~WP~d~~~~p~s~~~lRLI---~~GriL~d-~~tL~~~~~~ 72 (111)
T PF13881_consen 2 KIELKFRLADGKDIGPFRFDPSTTVADLKERIWAEWPEDWEERPKSPSDLRLI---YAGRILED-NKTLSDCRLP 72 (111)
T ss_dssp SEEEEEEETTS-EEEEEEE-TTSBHHHHHHHHHHSSSTTSSSTT-SGGGEEEE---ETTEEE-S-SSBTGGGT--
T ss_pred eEEEEEEEeCCCcccccccCccChHHHHHHHHHHHCccccccCCCChhhEEEE---eCCeecCC-cCcHHHhCCC
Confidence 467999999999 88999999999999999999877654 1224454 45667775 6899999877
No 37
>cd01769 UBL Ubiquitin-like domain of UBL. UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.
Probab=95.62 E-value=0.065 Score=38.52 Aligned_cols=64 Identities=17% Similarity=0.310 Sum_probs=48.4
Q ss_pred EEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC-eeEEe
Q 022009 235 IRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVIQ 302 (304)
Q Consensus 235 IRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~ivq 302 (304)
||..+|..+...+..+.||++|+..|.....-......|+ |-.+.|.| +.||.++++.+ +.|+.
T Consensus 2 v~~~~~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l~---~~g~~l~d-~~~l~~~~v~~~~~i~v 66 (69)
T cd01769 2 VKTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLI---YAGKILKD-DKTLSDYGIQDGSTLHL 66 (69)
T ss_pred eEccCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEE---ECCcCCCC-cCCHHHCCCCCCCEEEE
Confidence 6777899999999999999999999987653323344552 55677865 68999999996 55544
No 38
>cd01802 AN1_N ubiquitin-like domain of AN1. AN1 (also known as ANUBL1 and RSD-7) is ubiquitin-like protein with a testis-specific expression in rats that has an N-terminal ubiquitin-like domain and a C-terminal zinc-binding domain. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal ubiquitin-like domain of An1 does not undergo proteolytic processing. The function of AN1 is unknown.
Probab=95.61 E-value=0.072 Score=43.10 Aligned_cols=69 Identities=12% Similarity=0.124 Sum_probs=55.3
Q ss_pred CCceeEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC-eeE
Q 022009 228 LPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV 300 (304)
Q Consensus 228 ~p~t~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~i 300 (304)
.++-.|-||..+|+.+.+.+..++||.+|++.|.....-......|+ |=.+.|.|. .||++.++.+ ++|
T Consensus 25 ~~~M~I~Vk~l~G~~~~leV~~~~TV~~lK~kI~~~~gip~~~QrLi---~~Gk~L~D~-~tL~dy~I~~~stL 94 (103)
T cd01802 25 YDTMELFIETLTGTCFELRVSPFETVISVKAKIQRLEGIPVAQQHLI---WNNMELEDE-YCLNDYNISEGCTL 94 (103)
T ss_pred CCCEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEE---ECCEECCCC-CcHHHcCCCCCCEE
Confidence 34578999999999999999999999999999987543224456664 678889875 8999999995 444
No 39
>cd01797 NIRF_N amino-terminal ubiquitin-like domain of Np95 and NIRF. NIRF_N This CD represents the amino-terminal ubiquitin-like domain of a family of nuclear proteins that includes Np95 and NIRF (Np95/ICBP90-like RING finger) protein. Both Np95 and NIRF have a domain architecture consisting of a ubiquitin-like domain, a PHD finger, a YDG/SRA domain, Rb-binding motifs and a RING finger domain. Both Np95 and NIRF are ubiquitin ligases that ubiquitinate PCNP (PEST-containing nuclear proteins). While Np95 is capable of binding histones, NIRF is involved in cell cycle regulation.
Probab=95.43 E-value=0.085 Score=40.40 Aligned_cols=66 Identities=14% Similarity=0.174 Sum_probs=50.5
Q ss_pred eEEEEcCCCCE-EEE-ecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC-eeEE
Q 022009 232 SVQIRLADGTR-LIA-HFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI 301 (304)
Q Consensus 232 ~IqIRl~dG~r-l~~-rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~iv 301 (304)
.|-||..+|+. ... ....++||++|++.|.....-......|+ |=.|.|.| +.||.+.|+.+ ++|.
T Consensus 2 ~I~vk~~~G~~~~~l~~v~~~~TV~~lK~~i~~~~gi~~~~QrLi---~~Gk~L~D-~~tL~~y~i~~~~~i~ 70 (78)
T cd01797 2 WIQVRTMDGKETRTVDSLSRLTKVEELREKIQELFNVEPECQRLF---YRGKQMED-GHTLFDYNVGLNDIIQ 70 (78)
T ss_pred EEEEEcCCCCEEEEeeccCCcCcHHHHHHHHHHHhCCCHHHeEEE---eCCEECCC-CCCHHHcCCCCCCEEE
Confidence 47899999997 456 47889999999999987542224456664 67899987 58999999996 5554
No 40
>cd01763 Sumo Small ubiquitin-related modifier (SUMO). Small ubiquitin-related modifier (SUMO) proteins are conjugated to numerous intracellular targets and serve to modulate protein interaction, localization, activity or stability. SUMO (also known as "Smt3" and "sentrin" in other organisms) is linked to several different pathways, including nucleocytoplasmic transport. Attachment of SUMO to targets proteins is stimulated by PIAS (Protein inhibitor of activated STATs) proteins which serve as E3-like ligases.
Probab=95.05 E-value=0.19 Score=39.07 Aligned_cols=67 Identities=10% Similarity=0.184 Sum_probs=54.5
Q ss_pred CCCceeEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC
Q 022009 227 NLPSTSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN 297 (304)
Q Consensus 227 ~~p~t~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n 297 (304)
.....+|.|+..+|+.+..++..++||..|.+.+.....-....+.|+ |=-+.|.+ ..|+++++|.+
T Consensus 8 ~~~~i~I~v~~~~g~~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~---f~G~~L~~-~~T~~~l~m~d 74 (87)
T cd01763 8 ISEHINLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFL---FDGQRIRD-NQTPDDLGMED 74 (87)
T ss_pred CCCeEEEEEECCCCCEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEE---ECCeECCC-CCCHHHcCCCC
Confidence 345677889999999999999999999999999887654435566663 67888887 47999999996
No 41
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=94.85 E-value=0.1 Score=51.54 Aligned_cols=66 Identities=14% Similarity=0.308 Sum_probs=52.8
Q ss_pred eEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCC--C-CCCeEEEecCCCCccccCCCCchhhhCCCC-eeEE
Q 022009 232 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPG--T-ARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI 301 (304)
Q Consensus 232 ~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~--~-~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~iv 301 (304)
+|-||..+|+.+.+.+..++||.+|+..|...... . .....|+ |-.|.|.|. .||++++|.+ .+||
T Consensus 2 kItVKtl~g~~~~IeV~~~~TV~dLK~kI~~~~g~~~ip~~~QkLI---y~GkiL~Dd-~tL~dy~I~e~~~Iv 71 (378)
T TIGR00601 2 TLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLI---YSGKILSDD-KTVREYKIKEKDFVV 71 (378)
T ss_pred EEEEEeCCCCEEEEEeCCcChHHHHHHHHHHhhCCCCCChhHeEEE---ECCEECCCC-CcHHHcCCCCCCEEE
Confidence 58899999999999999999999999999876431 2 3345563 779999874 7999999984 5554
No 42
>PF11976 Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; InterPro: IPR022617 This entry includes small ubiquitin-related modifier (SUMO) proteins. SUMOs are small proteins that are covalently attached to lysines as post-translational modifications and are used to control multiple cellular process including signal transduction, nuclear transport and DNA replication and repair []. Unlike ubiquitin, they are not involved in protein degradation. This entry also contains the C-terminal Rad60 DNA repair protein SUMO-like domain.; PDB: 3RD2_A 2JXX_A 3RCZ_A 3GOE_A 3A4S_D 3A4R_B 2IO1_D 1U4A_A 2K1F_A 1WZ0_A ....
Probab=93.87 E-value=0.25 Score=36.48 Aligned_cols=62 Identities=19% Similarity=0.263 Sum_probs=49.3
Q ss_pred eEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCC-CCeEEEecCCCCccccCCCCchhhhCCCC
Q 022009 232 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTA-RNYQLQMMGFPPKVLADRTQTIEQAGLAN 297 (304)
Q Consensus 232 ~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~-~~f~L~t~~fP~k~l~d~s~TL~eagL~n 297 (304)
+|.||..+|+.+..+...++||+.|.+.+.....-.. ..+.|. |=.+.|.. +.|++++||..
T Consensus 2 ~i~v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~---fdG~~L~~-~~T~~~~~ied 64 (72)
T PF11976_consen 2 TIKVRSQDGKEIKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLI---FDGKRLDP-NDTPEDLGIED 64 (72)
T ss_dssp EEEEEETTSEEEEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEE---ETTEEE-T-TSCHHHHT-ST
T ss_pred EEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCccceEEEE---ECCEEcCC-CCCHHHCCCCC
Confidence 6889999999999999999999999988877543334 567773 78888875 47999999996
No 43
>cd01793 Fubi Fubi ubiquitin-like protein. Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.
Probab=93.87 E-value=0.29 Score=36.63 Aligned_cols=63 Identities=17% Similarity=0.211 Sum_probs=46.7
Q ss_pred eEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC-eeE
Q 022009 232 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV 300 (304)
Q Consensus 232 ~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~i 300 (304)
.|-||. ++.....+..++||++|..-|.....-......|+ |=.|.|.|. .||+++++.+ ++|
T Consensus 2 qi~vk~--~~~~~l~v~~~~tV~~lK~~i~~~~gip~~~q~Li---~~Gk~L~D~-~tL~~~~i~~~~tl 65 (74)
T cd01793 2 QLFVRA--QNTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVLL---LAGVPLEDD-ATLGQCGVEELCTL 65 (74)
T ss_pred EEEEEC--CCEEEEEECCcCcHHHHHHHHHhhhCCCHHHEEEE---ECCeECCCC-CCHHHcCCCCCCEE
Confidence 356665 46678899999999999999987532223345553 678999875 8999999986 544
No 44
>cd01790 Herp_N Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein. Herp (Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein) , is an integral membrane protein that is induced by the endoplasmic reticulum (ER) stress response pathway and is involved in improving the balance of folding capacity and protein loads in the ER. Herp has an N-terminal ubiquitin-like domain that is involved in Herp degradation, but is not necessary for its enhancement of amyloid beta-protein generation.
Probab=93.59 E-value=0.33 Score=37.60 Aligned_cols=60 Identities=13% Similarity=0.264 Sum_probs=46.6
Q ss_pred eeEEEEcCCCCE--EEEecCCCCCHHHHHHHHHhhCCCC--CCCeEEEecCCCCccccCCCCchhhhC
Q 022009 231 TSVQIRLADGTR--LIAHFNLHHTISDIHSFIDASRPGT--ARNYQLQMMGFPPKVLADRTQTIEQAG 294 (304)
Q Consensus 231 t~IqIRl~dG~r--l~~rFn~s~TV~dvr~fv~~~~~~~--~~~f~L~t~~fP~k~l~d~s~TL~eag 294 (304)
.+|.||.++|+. +...+..+.||.+|.+-|....+.. ...-.|+ |--|.|.| +.||++..
T Consensus 2 i~l~IK~~~~~~~~~~ve~~~~~TV~~lK~~i~~~~~~~~~~~~QrLI---y~GKiLkD-~~tL~~~~ 65 (79)
T cd01790 2 VTLLIKSPNQKYEDQTVSCFLNWTVGELKTHLSRVYPSKPLEQDQRLI---YSGKLLPD-HLKLRDVL 65 (79)
T ss_pred eEEEEECCCCCeEEEEEecCCcChHHHHHHHHHHhcCCCCChhHeEEE---EcCeeccc-hhhHHHHh
Confidence 478999999999 5555589999999999999865432 2334553 78899987 48999985
No 45
>cd01800 SF3a120_C Ubiquitin-like domain of Mammalian splicing factor SF3a_120. SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus.
Probab=93.59 E-value=0.23 Score=37.55 Aligned_cols=59 Identities=20% Similarity=0.279 Sum_probs=45.2
Q ss_pred CCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC-eeEE
Q 022009 239 DGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI 301 (304)
Q Consensus 239 dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~iv 301 (304)
+|+.+.+.+..+.||++|.+-|.....-......|+ |-.+.|.| +.||.+.++.+ ++|.
T Consensus 6 ~g~~~~l~v~~~~TV~~lK~~i~~~~gip~~~q~L~---~~G~~L~d-~~tL~~~~i~~g~~l~ 65 (76)
T cd01800 6 NGQMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQ---YEGIFIKD-SNSLAYYNLANGTIIH 65 (76)
T ss_pred CCeEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEE---ECCEEcCC-CCcHHHcCCCCCCEEE
Confidence 688889999999999999999987643224456664 45677877 48999999996 5553
No 46
>cd01813 UBP_N UBP ubiquitin processing protease. The UBP (ubiquitin processing protease) domain (also referred to as USP which stands for "ubiquitin-specific protease") is present at in a large family of cysteine proteases that specifically cleave ubiquitin conjugates. This family includes Rpn11, UBP6 (USP14), USP7 (HAUSP). This domain is closely related to the amino-terminal ubiquitin-like domain of BAG1 (Bcl2-associated anthanogene1) protein and is found only in eukaryotes.
Probab=93.28 E-value=0.56 Score=35.48 Aligned_cols=68 Identities=16% Similarity=0.167 Sum_probs=48.5
Q ss_pred eEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC-eeEE
Q 022009 232 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI 301 (304)
Q Consensus 232 ~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~iv 301 (304)
+|.|++ .|+.....+..++||++|.+-|.....-....-.|+-..|=.+.+.| +.||.++++.+ +.|+
T Consensus 2 ~i~vk~-~g~~~~v~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~~~~~Gk~l~D-~~~L~~~~i~~g~~i~ 70 (74)
T cd01813 2 PVIVKW-GGQEYSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLGLKVKGKPAED-DVKISALKLKPNTKIM 70 (74)
T ss_pred EEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEeecccCCcCCC-CcCHHHcCCCCCCEEE
Confidence 577777 77788899999999999999998864322445666510123455665 68999999985 4444
No 47
>cd00196 UBQ Ubiquitin-like proteins. Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate.
Probab=91.94 E-value=0.34 Score=32.14 Aligned_cols=60 Identities=18% Similarity=0.222 Sum_probs=42.7
Q ss_pred EEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC
Q 022009 234 QIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN 297 (304)
Q Consensus 234 qIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n 297 (304)
+|++.+|+....+++...||++|+++|..........|.|.. ..+.. .+ ..++.+.++..
T Consensus 1 ~v~~~~~~~~~~~~~~~~tv~~l~~~i~~~~~~~~~~~~l~~-~~~~~--~~-~~~~~~~~~~~ 60 (69)
T cd00196 1 KVKLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLV-NGKIL--PD-SLTLEDYGLQD 60 (69)
T ss_pred CeEecCCCEEEEEcCCCCcHHHHHHHHHHHHCcChHHeEEEE-CCeEC--CC-CCcHHHcCCCC
Confidence 367789999999999999999999999887543356788875 44432 22 23445556654
No 48
>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HOIL-1 (heme-oxidized IRP2 ubiquitin ligase-1) is an E3 ubiquitin-protein ligase that recognizes heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. Hoil-1 has an amino-terminal ubiquitin-like domain as well as an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain.
Probab=89.94 E-value=1 Score=34.18 Aligned_cols=57 Identities=9% Similarity=0.018 Sum_probs=42.5
Q ss_pred EcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCC
Q 022009 236 RLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLA 296 (304)
Q Consensus 236 Rl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~ 296 (304)
++..|..+...+..+.||++|...|.....-......| |-.+.|.++..||++.|+.
T Consensus 8 ~~~~~~t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL----~~G~~L~dD~~tL~~ygi~ 64 (75)
T cd01799 8 AQSHTVTIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRW----VIGQRLARDQETLYSHGIR 64 (75)
T ss_pred cccCCCeEEEEECCCCcHHHHHHHHHHHHCcCHHHEEE----EcCCeeCCCcCCHHHcCCC
Confidence 34557778899999999999999998653222333444 4566787777999999999
No 49
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=89.12 E-value=1 Score=43.57 Aligned_cols=69 Identities=10% Similarity=0.222 Sum_probs=55.0
Q ss_pred eEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCC-CCCCeEEEecCCCCccccCCCCchhhhCCC-CeeEEee
Q 022009 232 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPG-TARNYQLQMMGFPPKVLADRTQTIEQAGLA-NSVVIQK 303 (304)
Q Consensus 232 ~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~-~~~~f~L~t~~fP~k~l~d~s~TL~eagL~-na~ivqk 303 (304)
+|-||...|+...++++.+|||.+|..=|...... +...+.... |-.|.|.| +.||.+.++. +..||.+
T Consensus 2 ~lt~KtL~q~~F~iev~Pe~tV~evK~kIet~~g~dyP~~~QkLI--y~GkiL~D-~~tv~Eykv~E~~fiVvM 72 (340)
T KOG0011|consen 2 KLTVKTLKQQTFTIEVKPEDTVVEVKKKIETEKGPDYPAEQQKLI--YSGKILKD-ETTVGEYKVKEKKFIVVM 72 (340)
T ss_pred eeEeeeccCceeEeecCcchhHHHHHHHHHhccCCCCchhhheee--ecceeccC-CcchhhhccccCceEEEE
Confidence 57899999999999999999999999999876532 344555554 78899988 5899999999 4555543
No 50
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=88.75 E-value=1.9 Score=33.30 Aligned_cols=69 Identities=14% Similarity=0.204 Sum_probs=47.9
Q ss_pred eeEEEEcCCCC--EEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEec----CCCCccccCCCCchhhhCCCCee
Q 022009 231 TSVQIRLADGT--RLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMM----GFPPKVLADRTQTIEQAGLANSV 299 (304)
Q Consensus 231 t~IqIRl~dG~--rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~----~fP~k~l~d~s~TL~eagL~na~ 299 (304)
.+|.|.-..-+ ....||+.+.||++|..-|.....-......|... .-+...+.|+.+||...|+.+..
T Consensus 2 v~l~It~~~~~~~~~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~~~~~~~~~~~~~dd~~~L~~y~~~dg~ 76 (87)
T PF14560_consen 2 VKLFITSSNSKQRSVEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLKSDKDDSKIEELDDDDATLGSYGIKDGM 76 (87)
T ss_dssp EEEEEEESSSSSSEEEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE-TSSSSEEEESSGSSSBCCHHT-STTE
T ss_pred EEEEEEeCCCCCeeEEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEEecCCCccccccCCCccEeecCCCCCCC
Confidence 45777776664 78999999999999999998875444555666531 01113355778999999999733
No 51
>cd01795 USP48_C USP ubiquitin-specific protease. The USP (ubiquitin-specific protease) family is one of at least seven deubiquitylating enzyme (DUB) families capable of deconjugating ubiquitin and ubiquitin-like adducts. While the USP's have a conserved catalytic core domain, they differ in their domain architectures. This subfamily, which includes USP31, and USP48, has a carboxy-terminal ubiquitin-like domain in addition to a DUSP (domain of ubiquitin-specific proteases) domain,
Probab=87.52 E-value=1.6 Score=35.45 Aligned_cols=55 Identities=18% Similarity=0.283 Sum_probs=42.7
Q ss_pred EEEecCCCCCHHHHHHHHHhhCCCCCCCe--EEEecCCCCccccCCCCchhhhCCCC-eeEEe
Q 022009 243 LIAHFNLHHTISDIHSFIDASRPGTARNY--QLQMMGFPPKVLADRTQTIEQAGLAN-SVVIQ 302 (304)
Q Consensus 243 l~~rFn~s~TV~dvr~fv~~~~~~~~~~f--~L~t~~fP~k~l~d~s~TL~eagL~n-a~ivq 302 (304)
+.+..+.++||++|..-|..+-. ..+| .|+. . -+.|+|++.||.+.||.. |+|..
T Consensus 17 ~~L~V~~~~TVg~LK~lImQ~f~--V~P~dQkL~~-d--G~~L~DDsrTLssyGv~sgSvl~L 74 (107)
T cd01795 17 KALLVSANQTLKELKIQIMHAFS--VAPFDQNLSI-D--GKILSDDCATLGTLGVIPESVILL 74 (107)
T ss_pred ceEEeCccccHHHHHHHHHHHhc--CCcccceeee-c--CceeccCCccHHhcCCCCCCEEEE
Confidence 35668999999999999988643 3455 5653 3 679999999999999997 65544
No 52
>PLN02560 enoyl-CoA reductase
Probab=86.46 E-value=3.9 Score=39.37 Aligned_cols=71 Identities=18% Similarity=0.272 Sum_probs=47.0
Q ss_pred eEEEEcCCCCEE---EEecCCCCCHHHHHHHHHhhCCC-CCCCeEEEec---CCCCc-cccCCCCchhhhCCCC-eeEEe
Q 022009 232 SVQIRLADGTRL---IAHFNLHHTISDIHSFIDASRPG-TARNYQLQMM---GFPPK-VLADRTQTIEQAGLAN-SVVIQ 302 (304)
Q Consensus 232 ~IqIRl~dG~rl---~~rFn~s~TV~dvr~fv~~~~~~-~~~~f~L~t~---~fP~k-~l~d~s~TL~eagL~n-a~ivq 302 (304)
+|.|+..+|+.+ .+.+..+.||+||..-|.+...- ....-.|... +=|+. .|. ++.||++.|+.+ ++|..
T Consensus 2 ~I~Vk~~~Gk~i~~~~lev~~~aTV~dLK~~Isk~~~~~~~~RqRL~~~~~~gk~~g~~L~-d~ktL~d~gv~~gstLy~ 80 (308)
T PLN02560 2 KVTVVSRSGREIIKGGLEVPDSATVADLKKAIHKRKKKYYPSRQRLTLPLPPGKTRPTVLD-DSKSLKDYGLGDGGTVVF 80 (308)
T ss_pred EEEEEcCCCCeecceeEEcCCCCcHHHHHHHHHHHcCCCChhheEEEEecCCCCcCccccC-CCCCHHhcCCCCCceEEE
Confidence 477888888876 57889999999999999876432 1223344310 00222 344 467999999985 66665
Q ss_pred e
Q 022009 303 K 303 (304)
Q Consensus 303 k 303 (304)
|
T Consensus 81 k 81 (308)
T PLN02560 81 K 81 (308)
T ss_pred E
Confidence 4
No 53
>PF14836 Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A3O_B 3PPA_A 3T9L_A 4A3P_A 3PV1_A.
Probab=85.74 E-value=3.4 Score=32.77 Aligned_cols=56 Identities=20% Similarity=0.127 Sum_probs=32.7
Q ss_pred EEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCC--ccccCCCCchhhhCCCCe
Q 022009 242 RLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPP--KVLADRTQTIEQAGLANS 298 (304)
Q Consensus 242 rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~--k~l~d~s~TL~eagL~na 298 (304)
-+...|...+||+.|...+...-.- ...-.|-....+. -.|.+..+||+||||+..
T Consensus 15 ~~t~~FSk~DTI~~v~~~~rklf~i-~~E~RLW~~~~~~~~e~L~~~~~Tv~da~L~~g 72 (88)
T PF14836_consen 15 VLTKQFSKTDTIGFVEKEMRKLFNI-QEETRLWNKYSENSYELLNNPEITVEDAGLYDG 72 (88)
T ss_dssp EEEEEE-TTSBHHHHHHHHHHHCT--TS-EEEEEECTTTCEEEE--TTSBTTTTT--TT
T ss_pred HhHhhccccChHHHHHHHHHHHhCC-CccceehhccCCcchhhhCCCCccHHHccCcCC
Confidence 4688999999999999998875322 2222332212222 224577899999999963
No 54
>PF08817 YukD: WXG100 protein secretion system (Wss), protein YukD; InterPro: IPR014921 YukD is a bacterial protein that adopts a ubiquitin-like fold []. Ubiquitin covalently binds to protein and flags them for protein degradation, however conjugation assays have indicated that YukD lacks the capacity for covalent bond formation with other proteins []. ; PDB: 2BPS_B.
Probab=85.51 E-value=2.9 Score=31.76 Aligned_cols=69 Identities=13% Similarity=0.170 Sum_probs=44.9
Q ss_pred ceeEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCC----C--CCeEEEecCCCCccccCCCCchhhhCCCC-eeEE
Q 022009 230 STSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGT----A--RNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVI 301 (304)
Q Consensus 230 ~t~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~----~--~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~iv 301 (304)
.|+|-|...+|+++-+.+..+.||++|..-|....... . ..|.|. .-..+.|.+ +.||.++|+.+ .+++
T Consensus 2 ~~rVtv~~~~~~~~Dl~lP~~vpv~~li~~l~~~~~~~~~~~~~~~~~~L~--~~~g~~L~~-~~tL~~~gV~dGd~L~ 77 (79)
T PF08817_consen 2 LCRVTVDAGNGRQVDLALPADVPVAELIPELVELLGLPGDDPPGHGQWVLA--RAGGRPLDP-DQTLADAGVRDGDVLV 77 (79)
T ss_dssp EEEEEEE-TT--EEEEEEETTSBTTHHHHHHHHHS---S---TT-E-EEEG---GGTEEEET-TSBCGGGT--TT-EEE
T ss_pred EEEEEEEcCCCcEEEEEcCCCCcHHHHHHHHHHHhCCccCCCCCcceEEEE--ecCCcccCC-cCcHhHcCCCCCCEEE
Confidence 47889999888999999999999999988877643321 1 147774 245666665 68999999997 4443
No 55
>PF11470 TUG-UBL1: GLUT4 regulating protein TUG; InterPro: IPR021569 TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly. TUG releases the GLUT4 containing vesicles to the cellular exocytic machinery in response to insulin stimulation which allows translocation to the plasma membrane []. TUG has an N-terminal ubiquitin-like domain (UBL1) which in similar proteins appears to participate in protein-protein interactions []. The region does have a area of negative electrostatic potential and increased backbone motility which leads to suggestions of a potential protein-protein interaction site []. ; PDB: 2AL3_A.
Probab=82.31 E-value=4.5 Score=30.15 Aligned_cols=60 Identities=15% Similarity=0.116 Sum_probs=37.4
Q ss_pred cCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC-eeE
Q 022009 237 LADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV 300 (304)
Q Consensus 237 l~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~i 300 (304)
.++++|...+..+++|+.+|.+-+...-.-....|.|. +=+|.| |.+.++.-+||.| |.+
T Consensus 3 ~~~~rr~~vkvtp~~~l~~VL~eac~k~~l~~~~~~L~---h~~k~l-dlslp~R~snL~n~akL 63 (65)
T PF11470_consen 3 CYNFRRFKVKVTPNTTLNQVLEEACKKFGLDPSSYDLK---HNNKPL-DLSLPFRLSNLPNNAKL 63 (65)
T ss_dssp -TTS-EEEE---TTSBHHHHHHHHHHHTT--GGG-EEE---ETTEEE-SSS-BHHHH---SS-EE
T ss_pred ccCCcEEEEEECCCCCHHHHHHHHHHHcCCCccceEEE---ECCEEe-ccccceeecCCCCCCEE
Confidence 47899999999999999999988776644445689986 456776 5789999999997 543
No 56
>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-terminal domain of Tsc13. Tsc13 is an enoyl reductase involved in elongation of long chain fatty acids that localizes to the endoplasmic reticulum and is highly enriched in a novel structure marking nuclear-vacuolar junctions.
Probab=82.19 E-value=9.1 Score=28.78 Aligned_cols=54 Identities=22% Similarity=0.319 Sum_probs=37.6
Q ss_pred CCCCCHHHHHHHHHhhCCCC-CCCeEEEecCCCCccccCCCCchhhhCCCC-eeEEee
Q 022009 248 NLHHTISDIHSFIDASRPGT-ARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVVIQK 303 (304)
Q Consensus 248 n~s~TV~dvr~fv~~~~~~~-~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~ivqk 303 (304)
..+.||.||+..|....... .....|.. .+..+.|.|. .||.+.|+.+ ++|..|
T Consensus 20 ~~~aTV~dlk~~i~~~~~~~~~~Rqrl~~-~~~g~~L~d~-~tL~~~gv~~g~~lyvK 75 (77)
T cd01801 20 SGDATIADLKKLIAKSSPQLTVNRQSLRL-EPKGKSLKDD-DTLVDLGVGAGATLYVR 75 (77)
T ss_pred CCCccHHHHHHHHHHHcCCCCcceeEEEe-CCCCcccCCc-ccHhhcCCCCCCEEEEe
Confidence 46789999999998764322 23444543 5777888764 6899999986 556544
No 57
>PF09379 FERM_N: FERM N-terminal domain ; InterPro: IPR018979 This domain is the N-terminal ubiquitin-like structural domain of the FERM domain. The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane. Ezrin, a component of the undercoat of the microvilli plasma membrane. Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane. Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction. Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts. Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis. Merlin (or schwannomin). Protein NBL4. Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness. Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins. Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptors for cytokines or polypeptidic hormones. Non-receptor tyrosine-protein kinase TYK2. Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton. Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E. Caenorhabditis elegans protein phosphatase ptp-1. Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signalling pathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure []. The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].; PDB: 1EF1_B 1SGH_A 1E5W_A 2KC2_A 2KMA_A 3IVF_A 1H4R_B 3U8Z_A 1ISN_A 3BIN_A ....
Probab=81.23 E-value=1.7 Score=32.53 Aligned_cols=62 Identities=16% Similarity=0.097 Sum_probs=43.0
Q ss_pred EEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCC-CCCeEEEe-cCC-CCccccCCCCchhhhCCC
Q 022009 235 IRLADGTRLIAHFNLHHTISDIHSFIDASRPGT-ARNYQLQM-MGF-PPKVLADRTQTIEQAGLA 296 (304)
Q Consensus 235 IRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~-~~~f~L~t-~~f-P~k~l~d~s~TL~eagL~ 296 (304)
|+|+||+.+...++.+.|+++|.+.|.....-. ..-|.|.. ..- ....+-+.+.+|.+..-.
T Consensus 1 V~llD~~~~~~~v~~~~t~~~l~~~v~~~l~l~e~~~FgL~~~~~~~~~~~wL~~~k~l~~q~~~ 65 (80)
T PF09379_consen 1 VRLLDGTTKTFEVDPKTTGQDLLEQVCDKLGLKEKEYFGLQYQVDKDGEHHWLDLDKKLKKQLKK 65 (80)
T ss_dssp EEESSEEEEEEEEETTSBHHHHHHHHHHHHTTSSGGGEEEEE-EBTTSSEEEE-SSSBGGGSTBT
T ss_pred CCCcCCCcEEEEEcCCCcHHHHHHHHHHHcCCCCccEEEEEEeecCCCcceeccCcccHHHHcCC
Confidence 789999999999999999999999998864322 44577753 001 112233667788776554
No 58
>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B. Alp11, also known as tubulin-folding cofactor B, is one of at least three proteins required for the proper folding of tubulins prior to their incorporation into microtubules. These cofactors are necessary for the biogenesis of microtubules and for cell viability. Alp11 has three domains including an N-terminal ubiquitin-like domain (represented by this CD) which executes the essential function, a central coiled-coil domain necessary for maintenance of cellular alpha-tubulin levels, and a C-terminal CLIP-170 domain is required for efficient binding to alpha-tubulin.
Probab=80.69 E-value=9.4 Score=29.41 Aligned_cols=65 Identities=15% Similarity=0.214 Sum_probs=45.9
Q ss_pred eeEEEEcCC-CCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCc-----cccCCCCchhhhCCCC
Q 022009 231 TSVQIRLAD-GTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPK-----VLADRTQTIEQAGLAN 297 (304)
Q Consensus 231 t~IqIRl~d-G~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k-----~l~d~s~TL~eagL~n 297 (304)
.+|.|.... ......||..+.||++|.+=+.....-....-.|.. |..+ .|.++..+|..-|+.+
T Consensus 2 v~v~i~~~~~~~~~ekr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l--~~~~~~~~~~l~~d~~~L~~y~~~d 72 (84)
T cd01789 2 VTVNITSSADSFSFEKKYSRGLTIAELKKKLELVVGTPASSMRLQL--FDGDDKLVSKLDDDDALLGSYPVDD 72 (84)
T ss_pred EEEEEEeCCCceeeeEecCCCCcHHHHHHHHHHHHCCCccceEEEE--EcCCCCeEeecCCCccEeeeccCCC
Confidence 346666643 334789999999999999998776433344455532 4554 5777889999999996
No 59
>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC_UbP (bone marrow stromal cell-derived ubiquitin-like protein) has an N-terminal ubiquitin-like (UBQ) domain and a C-terminal ubiquitin-associated (UBA) domain, a domain architecture similar to those of the UBIN, Chap1, and ubiquilin proteins. This CD represents the N-terminal ubiquitin-like domain.
Probab=79.70 E-value=5.8 Score=30.48 Aligned_cols=49 Identities=22% Similarity=0.281 Sum_probs=36.6
Q ss_pred CCCCCHHHHHHHHHhhCCCC---CCCeEEEecCCCCccccCCCCchhhhCCCC-eeE
Q 022009 248 NLHHTISDIHSFIDASRPGT---ARNYQLQMMGFPPKVLADRTQTIEQAGLAN-SVV 300 (304)
Q Consensus 248 n~s~TV~dvr~fv~~~~~~~---~~~f~L~t~~fP~k~l~d~s~TL~eagL~n-a~i 300 (304)
..++||.+|.+-|....++. ...+.|+ |=.|.|.| +.||++.|+.+ ++|
T Consensus 18 ~~~~TV~~LK~kI~~~~~egi~~~dqQrLI---y~GKiL~D-~~TL~dygI~~gstl 70 (75)
T cd01815 18 PGGYQVSTLKQLIAAQLPDSLPDPELIDLI---HCGRKLKD-DQTLDFYGIQSGSTI 70 (75)
T ss_pred CccCcHHHHHHHHHHhhccCCCChHHeEEE---eCCcCCCC-CCcHHHcCCCCCCEE
Confidence 35799999999998764322 2346664 78899987 48999999995 444
No 60
>smart00295 B41 Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
Probab=77.91 E-value=6.9 Score=33.90 Aligned_cols=64 Identities=19% Similarity=0.208 Sum_probs=45.8
Q ss_pred eeEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCC-CCCeEEEecCCCCccc---cCCCCchhhhCC
Q 022009 231 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGT-ARNYQLQMMGFPPKVL---ADRTQTIEQAGL 295 (304)
Q Consensus 231 t~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~-~~~f~L~t~~fP~k~l---~d~s~TL~eagL 295 (304)
..|+|.|+||+.+..+++.+.|+.+|.+.|.....-. ..-|.|.. .-+.... -+...+|.+...
T Consensus 4 ~~~~V~l~dg~~~~~~~~~~~t~~ev~~~v~~~~~l~~~~~F~L~~-~~~~~~~~~~l~~~~~l~~~~~ 71 (207)
T smart00295 4 RVLKVYLLDGTTLEFEVDSSTTAEELLETVCRKLGIRESEYFGLQF-EDPDEDLSHWLDPAKTLLDQDV 71 (207)
T ss_pred EEEEEEecCCCEEEEEECCCCCHHHHHHHHHHHhCCCccceeEEEE-EcCCCCcCeeCCCccCHHHhcC
Confidence 5799999999999999999999999999998865332 45677765 2332211 234566666554
No 61
>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=67.62 E-value=4.8 Score=30.24 Aligned_cols=24 Identities=29% Similarity=0.493 Sum_probs=22.4
Q ss_pred CCEEEEecCCCCCHHHHHHHHHhh
Q 022009 240 GTRLIAHFNLHHTISDIHSFIDAS 263 (304)
Q Consensus 240 G~rl~~rFn~s~TV~dvr~fv~~~ 263 (304)
|+.+..+.|.++||+|+...|++.
T Consensus 11 GKKVRvKCn~dDtiGD~KKliaaQ 34 (73)
T KOG3493|consen 11 GKKVRVKCNTDDTIGDLKKLIAAQ 34 (73)
T ss_pred CceEEEEeCCcccccCHHHHHHHh
Confidence 888999999999999999999875
No 62
>cd01777 SNX27_RA Ubiquitin domain of SNX27 (sorting nexin protein 27). SNX27_RA SNX27 (sorting nexin protein 27) belongs to a large family of endosome-localized proteins related to sorting nexin1 which is implicated in regulating membrane traffic. The domain architecture of SNX27 includes an amino-terminal PDZ domain, a PX (PhoX homologous) domain, and a carboxy-terminal RA (RAS-associated) domain.
Probab=66.64 E-value=11 Score=29.83 Aligned_cols=34 Identities=15% Similarity=0.195 Sum_probs=30.5
Q ss_pred eeEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhC
Q 022009 231 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASR 264 (304)
Q Consensus 231 t~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~ 264 (304)
..|+|=||||+++..+...+++..+|++-+...-
T Consensus 2 V~L~V~Lpdg~~i~V~v~~s~~a~~Vleav~~kl 35 (87)
T cd01777 2 VELRIALPDKATVTVRVRKNATTDQVYQALVAKA 35 (87)
T ss_pred eEEEEEccCCCEEEEEEEEcccHHHHHHHHHHHh
Confidence 4689999999999999999999999999887653
No 63
>cd01787 GRB7_RA RA (RAS-associated like) domain of Grb7. Grb7_RA The RA (RAS-associated like) domain of Grb7. Grb7 is an adaptor molecule that mediates signal transduction from multiple cell surface receptors to various downstream signaling pathways. Grb7 and its related family members Grb10 and Grb14 share a conserved domain architecture that includes an amino-terminal proline-rich region, a central segment termed the GM region (for Grb and Mig) which includes the RA, PIR, and PH domains, and a carboxyl-terminal SH2 domain. Grb7/10/14 family proteins are phosphorylated on serine/threonine as well as tyrosine residues and are mainly localized to the cytoplasm.
Probab=66.18 E-value=25 Score=27.75 Aligned_cols=55 Identities=15% Similarity=0.215 Sum_probs=43.8
Q ss_pred eeEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCC-CCCCeEEEecCCCCc----cccCC
Q 022009 231 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPG-TARNYQLQMMGFPPK----VLADR 286 (304)
Q Consensus 231 t~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~-~~~~f~L~t~~fP~k----~l~d~ 286 (304)
--|+|-++||+...+-+..++|++||-+.+.....- ....+.|+- ..|-- .|.|.
T Consensus 3 ~vvkv~~~Dg~sK~l~V~~~~Ta~dV~~~L~~K~h~~~~~~W~LvE-~~P~l~lER~~EDH 62 (85)
T cd01787 3 QVVKVYSEDGASKSLEVDERMTARDVCQLLVDKNHCQDDSSWTLVE-HLPHLQLERLFEDH 62 (85)
T ss_pred eEEEEEecCCCeeEEEEcCCCcHHHHHHHHHHHhCCCCCCCeEEEE-ecchhhhhhhccch
Confidence 357899999999999999999999999988765433 367899987 78864 45554
No 64
>cd01760 RBD Ubiquitin-like domain of RBD-like S/T kinases. The ras-binding domain (RBD) of the serine/threonine kinase raf is structurally quite similar to the beta-grasp fold of ubiquitin. A raf-like RBD is also present in RGS12 and other members of a family of GTPase activating proteins and TIAM1, a guanine nucleotide exchange protein.
Probab=59.55 E-value=27 Score=26.43 Aligned_cols=43 Identities=12% Similarity=0.166 Sum_probs=35.3
Q ss_pred EEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEe
Q 022009 233 VQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQM 275 (304)
Q Consensus 233 IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t 275 (304)
+.|=||||++-.....+.+||.|+..=+-..+.-....+.|..
T Consensus 2 ~~V~LPng~~t~V~vrpg~ti~d~L~~~c~kr~l~~~~~~v~~ 44 (72)
T cd01760 2 CRVYLPNGQRTVVPVRPGMSVRDVLAKACKKRGLNPECCDVFL 44 (72)
T ss_pred EEEECcCCCeEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEE
Confidence 5677999999999999999999999888777655455666654
No 65
>cd01818 TIAM1_RBD Ubiquitin domain of Tiam1 guanine nucleotide exchange factor. Tiam1 (T lymphoma invasion and metastasis 1) a guanine nucleotide exchange factor that activates Rac, is an important regulator of Rho GTPase functions in tumor cells including regulation of cell shape and invasiveness in epithelial cells and fibroblasts. TIAM1 has an RBD (Ras-binding domain) similar to that of Raf kinase as well as PH (pleckstrin homology), PDZ, and RhoGEF domains.
Probab=51.02 E-value=40 Score=26.09 Aligned_cols=41 Identities=10% Similarity=0.109 Sum_probs=32.7
Q ss_pred EEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEe
Q 022009 235 IRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQM 275 (304)
Q Consensus 235 IRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t 275 (304)
|=||||.+........+|+.||..-+.+.+.-....+.|..
T Consensus 4 V~lPn~~~~~v~vrp~~tv~dvLe~aCk~~~ldp~eh~Lrl 44 (77)
T cd01818 4 VCLPDNQPVLTYLRPGMSVEDFLESACKRKQLDPMEHYLRL 44 (77)
T ss_pred EECCCCceEEEEECCCCCHHHHHHHHHHhcCCChhHheeEE
Confidence 55999999999999999999999988776544455666653
No 66
>PF02196 RBD: Raf-like Ras-binding domain; InterPro: IPR003116 This is the Ras-binding domain found in proteins related to Ras. It is found in association with the PE-bind and pkinase domains.; GO: 0005057 receptor signaling protein activity, 0007165 signal transduction; PDB: 1RFA_A 1C1Y_B 3KUD_B 1GUA_B 3KUC_B 2L05_A 3NY5_D 1RRB_A 1WFY_A 1WXM_A.
Probab=49.88 E-value=67 Score=23.98 Aligned_cols=52 Identities=21% Similarity=0.275 Sum_probs=36.8
Q ss_pred eEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCcccc
Q 022009 232 SVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA 284 (304)
Q Consensus 232 ~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~ 284 (304)
.+++=||||++.........||.|+..-+-..+.-....+.+...+ ..+.|.
T Consensus 2 ~~~v~LP~~q~t~V~vrpg~ti~d~L~~~~~kr~L~~~~~~V~~~~-~~k~l~ 53 (71)
T PF02196_consen 2 TCRVHLPNGQRTVVQVRPGMTIRDALSKACKKRGLNPECCDVRLVG-EKKPLD 53 (71)
T ss_dssp EEEEEETTTEEEEEEE-TTSBHHHHHHHHHHTTT--CCCEEEEEEE-EEEEE-
T ss_pred eEEEECCCCCEEEEEEcCCCCHHHHHHHHHHHcCCCHHHEEEEEcC-CCcccc
Confidence 4788899999999999999999999988887765544555554323 555554
No 67
>PF13019 Telomere_Sde2: Telomere stability and silencing
Probab=48.12 E-value=76 Score=27.94 Aligned_cols=51 Identities=20% Similarity=0.205 Sum_probs=39.1
Q ss_pred eEEEEcCCC----CEEEEecCCCCCHHHHHHHHHhhCCCCCC-CeEEEecCCCCcccc
Q 022009 232 SVQIRLADG----TRLIAHFNLHHTISDIHSFIDASRPGTAR-NYQLQMMGFPPKVLA 284 (304)
Q Consensus 232 ~IqIRl~dG----~rl~~rFn~s~TV~dvr~fv~~~~~~~~~-~f~L~t~~fP~k~l~ 284 (304)
+|-|+..+| ..+.+.+..+.||.||++.|....+.... .+.|.+ ..++.|.
T Consensus 2 ~Vlvss~~g~~lp~tl~~~lp~~ttv~dL~~~l~~~~~~~~~~~~~L~~--~~n~~l~ 57 (162)
T PF13019_consen 2 NVLVSSFDGLTLPPTLSLSLPSTTTVSDLKDRLSERLPIPSSSQLYLTT--NSNGQLS 57 (162)
T ss_pred eEEEecCCCCCCCCeEEeeCCCCCcHHHHHHHHHhhcCCCccceeEEEE--eCCCeeC
Confidence 577899999 57888999999999999999987665522 366654 5666664
No 68
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=46.60 E-value=46 Score=34.18 Aligned_cols=63 Identities=13% Similarity=0.261 Sum_probs=50.2
Q ss_pred ceeEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCC
Q 022009 230 STSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLAN 297 (304)
Q Consensus 230 ~t~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~n 297 (304)
.++|.||.++. ...+....+.||.++..-|...-......-+| =|=-|.|.| ..||...|+..
T Consensus 15 ~irV~Vkt~~d-k~~~~V~~~ssV~qlKE~I~~~f~a~~dqlvL---IfaGrILKD-~dTL~~~gI~D 77 (493)
T KOG0010|consen 15 LIRVTVKTPKD-KYEVNVASDSSVLQLKELIAQRFGAPPDQLVL---IYAGRILKD-DDTLKQYGIQD 77 (493)
T ss_pred eeEEEEecCCc-ceeEecccchHHHHHHHHHHHhcCCChhHeee---eecCccccC-hhhHHHcCCCC
Confidence 47899999999 77889999999999999998754222333444 388999996 58999999996
No 69
>smart00455 RBD Raf-like Ras-binding domain.
Probab=45.48 E-value=64 Score=24.09 Aligned_cols=42 Identities=14% Similarity=0.150 Sum_probs=32.8
Q ss_pred EEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEE
Q 022009 233 VQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQ 274 (304)
Q Consensus 233 IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~ 274 (304)
+.+=||||++......+..||.|+..=+-+.+.-....+.|.
T Consensus 2 ~~v~LP~~~~~~V~vrpg~tl~e~L~~~~~kr~l~~~~~~v~ 43 (70)
T smart00455 2 CKVHLPDNQRTVVKVRPGKTVRDALAKALKKRGLNPECCVVR 43 (70)
T ss_pred eEEECCCCCEEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEE
Confidence 456799999999999999999999888877654434445554
No 70
>PF10302 DUF2407: DUF2407 ubiquitin-like domain; InterPro: IPR019413 This entry represents a family of proteins of unknown function found in fungi. They contain a characteristic GFDRL sequence motif.
Probab=42.48 E-value=86 Score=25.05 Aligned_cols=53 Identities=23% Similarity=0.344 Sum_probs=39.1
Q ss_pred eEEEEcCCCCE-EEEecC--CCCCHHHHHHHHHhhCCCC--CCCeEEEecCCCCccccCCC
Q 022009 232 SVQIRLADGTR-LIAHFN--LHHTISDIHSFIDASRPGT--ARNYQLQMMGFPPKVLADRT 287 (304)
Q Consensus 232 ~IqIRl~dG~r-l~~rFn--~s~TV~dvr~fv~~~~~~~--~~~f~L~t~~fP~k~l~d~s 287 (304)
.|-|||.++-. +.+.++ .+.||..|+..|....|.. .+.-.|+ |=-|.|.|.+
T Consensus 2 ~l~IRFs~sipDl~L~I~~~~~~Tv~~LK~lIR~~~p~~~s~~rLRlI---~~Gr~L~d~t 59 (97)
T PF10302_consen 2 YLTIRFSDSIPDLPLDIPSPNTTTVAWLKQLIRERLPPEPSRRRLRLI---YAGRLLNDHT 59 (97)
T ss_pred eEEEEECCCCCCceeecCCCCcccHHHHHHHHHhhcCCCCccccEEee---ecCcccCccc
Confidence 36788888543 778888 8899999999999988554 3344443 6778888753
No 71
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=35.08 E-value=1.3e+02 Score=22.09 Aligned_cols=43 Identities=14% Similarity=0.187 Sum_probs=33.3
Q ss_pred eeEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEE
Q 022009 231 TSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQ 274 (304)
Q Consensus 231 t~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~ 274 (304)
.+|++++ .|.....++...-|..+|++-|...-+.....|.|.
T Consensus 2 ~~vK~~~-~~~~~~~~~~~~~s~~dL~~~i~~~~~~~~~~~~l~ 44 (81)
T smart00666 2 VDVKLRY-GGETRRLSVPRDISFEDLRSKVAKRFGLDNQSFTLK 44 (81)
T ss_pred ccEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHhCCCCCCeEEE
Confidence 5678888 666677888889999999999988765434567774
No 72
>cd06536 CIDE_N_ICAD CIDE_N domain of ICAD. The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of the CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD (DFF45). These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of the CAD/DFF40 and ICAD/DFF45 during apoptosis. In normal cells, DFF exists in the nucleus as a heterodimer composed of CAD/DFF40 as a latent nuclease and its chaperone and inhibitor subunit ICAD/DFF45. Apoptotic activation of caspase-3 results in the cleavage of DFF45/ICAD and release of active DFF40/CAD nuclease.
Probab=34.08 E-value=21 Score=27.79 Aligned_cols=18 Identities=22% Similarity=0.272 Sum_probs=15.3
Q ss_pred eEEEEEeccceeecCCCC
Q 022009 117 VHNIVFWANGFTVNDGPL 134 (304)
Q Consensus 117 ~~~It~w~nGF~VdDGpf 134 (304)
.++|.|+.||..|||.+|
T Consensus 42 ~~~lvL~eDGT~VddEey 59 (80)
T cd06536 42 PITLVLAEDGTIVEDEDY 59 (80)
T ss_pred ceEEEEecCCcEEccHHH
Confidence 478999999999988554
No 73
>smart00537 DCX Domain in the Doublecortin (DCX) gene product. Tandemly-repeated domain in doublin, the Doublecortin gene product. Proposed to bind tubulin. Doublecortin (DCX) is mutated in human X-linked neuronal migration defects.
Probab=33.55 E-value=42 Score=26.20 Aligned_cols=35 Identities=17% Similarity=0.217 Sum_probs=22.5
Q ss_pred eEEEEEeccceeecCCCCccCC---ChhhHHHHHHHHc
Q 022009 117 VHNIVFWANGFTVNDGPLRRLD---DPENASFLESIKK 151 (304)
Q Consensus 117 ~~~It~w~nGF~VdDGpfR~yd---dP~n~~FL~~I~~ 151 (304)
...|+|||||=....|--...+ -+.-.+||++|.+
T Consensus 5 ~k~i~~~rNGD~~~~g~~~~v~~~~~~s~d~lL~~lt~ 42 (89)
T smart00537 5 PKRIRFYRNGDRFFKGVRLVVNRKRFKSFEALLQDLTE 42 (89)
T ss_pred ceEEEEEeCCCCCCCCEEEEEChhhcCCHHHHHHHHhh
Confidence 4689999999444444321111 2245689999988
No 74
>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....
Probab=32.50 E-value=1.1e+02 Score=22.61 Aligned_cols=45 Identities=20% Similarity=0.268 Sum_probs=34.6
Q ss_pred ceeEEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEE
Q 022009 230 STSVQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQ 274 (304)
Q Consensus 230 ~t~IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~ 274 (304)
+.+|.+++.+..+..+.+....+..+|+.-|....+.....|.|.
T Consensus 1 t~~vK~~~~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~ 45 (84)
T PF00564_consen 1 TVRVKVRYGGDIRRIISLPSDVSFDDLRSKIREKFGLLDEDFQLK 45 (84)
T ss_dssp SEEEEEEETTEEEEEEEECSTSHHHHHHHHHHHHHTTSTSSEEEE
T ss_pred CEEEEEEECCeeEEEEEcCCCCCHHHHHHHHHHHhCCCCccEEEE
Confidence 357888888877776888888899999999998655434677764
No 75
>KOG0005 consensus Ubiquitin-like protein [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=30.86 E-value=1.5e+02 Score=22.03 Aligned_cols=65 Identities=12% Similarity=0.234 Sum_probs=47.8
Q ss_pred EEEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCCCeeEE
Q 022009 233 VQIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLANSVVI 301 (304)
Q Consensus 233 IqIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~na~iv 301 (304)
|.++...|+.+.+-..++++|..|..-|.....-....-.| -|-.|.+.| ++|-+.-+|....|+
T Consensus 3 iKvktLt~KeIeidIep~DkverIKErvEEkeGIPp~qqrl---i~~gkqm~D-D~tA~~Y~~~~GSVl 67 (70)
T KOG0005|consen 3 IKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRL---IYAGKQMND-DKTAAHYNLLGGSVL 67 (70)
T ss_pred eeEeeeccceEEEeeCcchHHHHHHHHhhhhcCCCchhhhh---hhccccccc-cccHHHhhhccceeE
Confidence 67788899999999999999999999998653211222223 367788876 489999998864444
No 76
>cd01817 RGS12_RBD Ubiquitin domain of RGS12 and RGS14. RGS12 (regulator of G signalling 12), and RGS14, are members of a family of GTPase-activating proteins (GAP's) specific for the G-alpha subunit, which act as key inhibitors of G-protein-mediated cell responses in eukaryotes. Their domain architecture includes tandem RBD domains as well as PDZ , PTB, and RGS, and GoLoco domains.
Probab=30.11 E-value=1.8e+02 Score=22.27 Aligned_cols=58 Identities=17% Similarity=0.123 Sum_probs=38.0
Q ss_pred EEEcCCCCEEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCcccc--CCCCchhh
Q 022009 234 QIRLADGTRLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLA--DRTQTIEQ 292 (304)
Q Consensus 234 qIRl~dG~rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~--d~s~TL~e 292 (304)
+|=||||++-+....+-.||.|+..=+-..+.-....+.+.. .=-.|.|. .++.+|..
T Consensus 3 rV~LPdg~~T~V~vrpG~ti~d~L~kllekRgl~~~~~~vf~-~g~~k~l~~~qD~~~L~~ 62 (73)
T cd01817 3 RVILPDGSTTVVPTRPGESIRDLLSGLCEKRGINYAAVDLFL-VGGDKPLVLDQDSSVLAG 62 (73)
T ss_pred EEECCCCCeEEEEecCCCCHHHHHHHHHHHcCCChhHEEEEE-ecCCcccccCCccceeec
Confidence 566999999999999999999988777666644334444443 11124443 23455543
No 77
>cd01615 CIDE_N CIDE_N domain, found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins, as well as CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD(DFF45). These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of ICAD/DFF45, and the CAD/DFF40 and CIDE nucleases during apoptosis. The CIDE-N domain is also found in the FSP27/CIDE-C protein.
Probab=30.10 E-value=27 Score=27.06 Aligned_cols=18 Identities=22% Similarity=0.300 Sum_probs=15.2
Q ss_pred eEEEEEeccceeecCCCC
Q 022009 117 VHNIVFWANGFTVNDGPL 134 (304)
Q Consensus 117 ~~~It~w~nGF~VdDGpf 134 (304)
.++|.|+.||..|||.+|
T Consensus 40 ~~~lvL~eDGTeVddEeY 57 (78)
T cd01615 40 PVTLVLEEDGTEVDDEEY 57 (78)
T ss_pred CeEEEEeCCCcEEccHHH
Confidence 468999999999988554
No 78
>smart00266 CAD Domains present in proteins implicated in post-mortem DNA fragmentation.
Probab=29.71 E-value=27 Score=26.86 Aligned_cols=19 Identities=21% Similarity=0.219 Sum_probs=15.7
Q ss_pred eEEEEEeccceeecCCCCc
Q 022009 117 VHNIVFWANGFTVNDGPLR 135 (304)
Q Consensus 117 ~~~It~w~nGF~VdDGpfR 135 (304)
.++|.|+.||..|||.+|.
T Consensus 38 ~~~l~L~eDGT~VddEeyF 56 (74)
T smart00266 38 PVTLVLEEDGTIVDDEEYF 56 (74)
T ss_pred CcEEEEecCCcEEccHHHH
Confidence 4689999999999886653
No 79
>PF00788 RA: Ras association (RalGDS/AF-6) domain; InterPro: IPR000159 Proteins with this domain are mostly RasGTP effectors and include guanine-nucleotide releasing factor in mammals []. This factor stimulates the dissociation of GDP from the Ras-related RALA and RALB GTPases, which allows GTP binding and activation of the GTPases. It interacts and acts as an effector molecule for R-ras, K-Ras and Rap []. The domain is also present in a number of other proteins among them the sexual differentiation protein in yeast that is essential for mating and meiosis and yeast adenylate cyclase. These proteins contain repeated leucine-rich (LRR) segments.; GO: 0007165 signal transduction; PDB: 3EC8_A 2C5L_D 2BYF_A 2CS4_A 3KH0_A 2B3A_A 1RAX_A 2RGF_A 1WGR_A 1WXA_A ....
Probab=28.55 E-value=1.9e+02 Score=21.42 Aligned_cols=58 Identities=14% Similarity=0.072 Sum_probs=42.1
Q ss_pred ceeEEEEcCCCC----EEEEecCCCCCHHHHHHHHHhhCC--CCCCCeEE--EecCCCC--ccccCCCC
Q 022009 230 STSVQIRLADGT----RLIAHFNLHHTISDIHSFIDASRP--GTARNYQL--QMMGFPP--KVLADRTQ 288 (304)
Q Consensus 230 ~t~IqIRl~dG~----rl~~rFn~s~TV~dvr~fv~~~~~--~~~~~f~L--~t~~fP~--k~l~d~s~ 288 (304)
...|+|-..+++ ...+++..+.|+.+|..-+..... +....|.| .. .... |.|.+...
T Consensus 2 ~~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~~~~~y~L~~~~-~~~~~er~L~~~E~ 69 (93)
T PF00788_consen 2 SGVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAEDPSDYCLVEVE-ESGGEERPLDDDEC 69 (93)
T ss_dssp EEEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSSSGGGEEEEEEE-CTTTEEEEETTTSB
T ss_pred CeEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCCCCCCEEEEEEE-cCCCEEEEcCCCCc
Confidence 356899999999 999999999999999887765432 23678999 43 4444 44554433
No 80
>PF03562 MltA: MltA specific insert domain; InterPro: IPR005300 This group of proteins includes MltA; a membrane-bound, murein degrading transglycosylase enzyme which plays an important role in the controlled growth of the stress-bearing sacculus of Escherichia coli [, ].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds; PDB: 2PI8_D 2AE0_X 2PIC_A 2GAE_A 2PJJ_A 3CZB_A 2G6G_A 2PNW_A 2G5D_A.
Probab=28.25 E-value=90 Score=27.32 Aligned_cols=32 Identities=22% Similarity=0.528 Sum_probs=24.2
Q ss_pred EEEcCCCCEEEEecC----------------------CCCCHHHHHHHHHhhCCC
Q 022009 234 QIRLADGTRLIAHFN----------------------LHHTISDIHSFIDASRPG 266 (304)
Q Consensus 234 qIRl~dG~rl~~rFn----------------------~s~TV~dvr~fv~~~~~~ 266 (304)
+|||+||+.+.+-|. ...+.+.|++|+.++ |+
T Consensus 89 rl~l~DG~~~rvgYAg~NG~pY~sIGr~Li~~G~i~~~~~Smq~Ir~wl~~~-P~ 142 (158)
T PF03562_consen 89 RLRLPDGSTVRVGYAGQNGHPYTSIGRLLIDRGEIPREQMSMQAIRAWLRAH-PE 142 (158)
T ss_dssp EEE-TTSSEEEEEEEEE-SS----HHHHHHHTTSS-TTS-SHHHHHHHHHHT-GG
T ss_pred EEEcCCCCEEEEEEcccCCCccccHHHHHHHcCCcChhhCCHHHHHHHHHHC-HH
Confidence 789999998877765 467889999999876 44
No 81
>cd06538 CIDE_N_FSP27 CIDE_N domain of FSP27 proteins. The CIDE-N (cell death-inducing DFF45-like effector, N-terminal) domain is found in the FSP27/CIDE-C protein, which has been identified as a n adipocyte lipid droplet protein that negatively regulates lipolysis and promotes triglyceride accumulation. The CIDE protein family includes 3 members: CIDE-A, CIDE-B, and FSP27(CIDE-C). Based on sequence similarity with DFF40 and DFF45, CIDE proteins were initially characterized as mitochondrial activators of apoptosis. The CIDE-N domain of FSP27 is sufficient to increase apoptosis in vitro when overexpressed.
Probab=27.22 E-value=30 Score=26.93 Aligned_cols=17 Identities=18% Similarity=0.306 Sum_probs=14.5
Q ss_pred EEEEEeccceeecCCCC
Q 022009 118 HNIVFWANGFTVNDGPL 134 (304)
Q Consensus 118 ~~It~w~nGF~VdDGpf 134 (304)
++|.|+.||..|+|.+|
T Consensus 40 ~~lvL~eDGT~Vd~Eey 56 (79)
T cd06538 40 SSLVLDEDGTGVDTEEF 56 (79)
T ss_pred cEEEEecCCcEEccHHH
Confidence 68999999999988544
No 82
>COG5100 NPL4 Nuclear pore protein [Nuclear structure]
Probab=26.79 E-value=2.3e+02 Score=28.82 Aligned_cols=66 Identities=14% Similarity=0.220 Sum_probs=42.5
Q ss_pred EEEEcCCCCEEEEecCCCCCHHHHH----HHHHhhCCCCCCCeEEEecCCCC-ccc---cCCCCchhhhCCCC-eeEEee
Q 022009 233 VQIRLADGTRLIAHFNLHHTISDIH----SFIDASRPGTARNYQLQMMGFPP-KVL---ADRTQTIEQAGLAN-SVVIQK 303 (304)
Q Consensus 233 IqIRl~dG~rl~~rFn~s~TV~dvr----~fv~~~~~~~~~~f~L~t~~fP~-k~l---~d~s~TL~eagL~n-a~ivqk 303 (304)
+++|-..|++ .+.|..+++++-|- .|+... -....|.+.. -|. +-. ...++|+.++||.+ -++..+
T Consensus 3 ~rfRsk~G~~-Rve~qe~d~lg~l~~kll~~~~~n--~~~e~~svc~--~p~~qG~~~s~l~dqt~~dlGL~hGqmLyl~ 77 (571)
T COG5100 3 FRFRSKEGQR-RVEVQESDVLGMLSPKLLAFFEVN--YSPEQISVCS--APDGQGEIFSLLKDQTPDDLGLRHGQMLYLE 77 (571)
T ss_pred EEEecCCCce-eeeccccchhhhhhHHHHhhhccC--CCccceEEEe--CCCCCceeeecccccChhhhccccCcEEEEE
Confidence 7899999986 45788888887444 444322 1145677764 354 222 24579999999997 444443
No 83
>cd01788 ElonginB Ubiquitin-like domain of Elongin B. Elongin B is part of an E3 ubiquitin ligase complex called VEC that activates ubiquitylation by the E2 ubiquitin-conjugating enzyme Ubc5. VEC is composed of von Hippel-Lindau tumor suppressor protein (pVHL), elongin C, cullin 2, NEDD8, and Rbx1. ElonginB binds elonginC to form the elonginBC complex which is a positive regulator of RNA polymerase II elongation factor Elongin A. The BC complex then binds VHL (von Hippel-Lindau) tumour suppressor protein to form a VCB ternary complex. Elongin B has a ubiquitin-llike domain.
Probab=25.21 E-value=2.9e+02 Score=23.14 Aligned_cols=51 Identities=12% Similarity=0.285 Sum_probs=33.1
Q ss_pred EEEEecCCCCCHHHHHHHHHhhCCCCCCCeEEEecCCCCccccCCCCchhhhCCC
Q 022009 242 RLIAHFNLHHTISDIHSFIDASRPGTARNYQLQMMGFPPKVLADRTQTIEQAGLA 296 (304)
Q Consensus 242 rl~~rFn~s~TV~dvr~fv~~~~~~~~~~f~L~t~~fP~k~l~d~s~TL~eagL~ 296 (304)
.+-.....++||-+|..-|....-....+=.| |.--.+-|+++||.|+|+.
T Consensus 13 TiF~dakes~tVlelK~~iegI~k~pp~dQrL----~kd~qvLeD~kTL~d~g~t 63 (119)
T cd01788 13 TIFTDAKESTTVYELKRIVEGILKRPPEDQRL----YKDDQLLDDGKTLGDCGFT 63 (119)
T ss_pred EEEeecCCcccHHHHHHHHHHHhcCChhHhee----ecCceeecccccHHHcCcc
Confidence 34456678999999999887643222222233 3333555668999999993
No 84
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=23.45 E-value=1.2e+02 Score=21.52 Aligned_cols=27 Identities=19% Similarity=0.288 Sum_probs=24.1
Q ss_pred cCCCCEEEEecCCCCCHHHHHHHHHhh
Q 022009 237 LADGTRLIAHFNLHHTISDIHSFIDAS 263 (304)
Q Consensus 237 l~dG~rl~~rFn~s~TV~dvr~fv~~~ 263 (304)
+..|..+.+..+...++.+|..|+...
T Consensus 23 l~~g~~l~v~~d~~~~~~~i~~~~~~~ 49 (69)
T cd00291 23 LKSGEVLEVLLDDPGAVEDIPAWAKET 49 (69)
T ss_pred CCCCCEEEEEecCCcHHHHHHHHHHHc
Confidence 567999999999999999999999865
No 85
>cd01768 RA RA (Ras-associating) ubiquitin domain. The RA (Ras-associating) domain is structurally similar to ubiquitin and is present in one or two copies in a number of signalling molecules that bind and regulate a small GTPase called Ras or the Ras-related GTPases, Ral and Rap. RA-containing proteins include RalGDS, AF6, RIN1, RASSF1, SNX27, CYR1, STE50, and phospholipase C epsilon.
Probab=22.31 E-value=3.2e+02 Score=20.37 Aligned_cols=58 Identities=14% Similarity=0.153 Sum_probs=39.4
Q ss_pred EEEEcCC---CCEEEEecCCCCCHHHHHHHHHhh-CCC-CCCCeEEEecCCCC----ccccCCCCchh
Q 022009 233 VQIRLAD---GTRLIAHFNLHHTISDIHSFIDAS-RPG-TARNYQLQMMGFPP----KVLADRTQTIE 291 (304)
Q Consensus 233 IqIRl~d---G~rl~~rFn~s~TV~dvr~fv~~~-~~~-~~~~f~L~t~~fP~----k~l~d~s~TL~ 291 (304)
|+|-..| ++...++...+.|..+|..-+... .-. ....|.|.. -.+. |.|.+...-|.
T Consensus 2 ikV~~~~~~~~~~kti~V~~~~t~~~Vi~~~l~k~~l~~~~~~y~L~e-v~~~~~~er~L~~~e~pl~ 68 (87)
T cd01768 2 LRVYPEDPSGGTYKTLRVSKDTTAQDVIQQLLKKFGLDDDPEDYALVE-VLGDGGLERLLLPDECPLQ 68 (87)
T ss_pred EEEeCCcCCCccEEEEEECCCCCHHHHHHHHHHHhCCcCCcccEEEEE-EECCceEEEEeCCCCChHH
Confidence 5566666 888999999999999998776553 222 367899975 3444 44555555443
No 86
>KOG0625 consensus Phosphoglucomutase [Carbohydrate transport and metabolism]
Probab=21.09 E-value=37 Score=34.47 Aligned_cols=35 Identities=17% Similarity=0.386 Sum_probs=28.8
Q ss_pred eEEEEcCCCCEEEEecCCCCCH-HHHHHHHHhhCCC
Q 022009 232 SVQIRLADGTRLIAHFNLHHTI-SDIHSFIDASRPG 266 (304)
Q Consensus 232 ~IqIRl~dG~rl~~rFn~s~TV-~dvr~fv~~~~~~ 266 (304)
-|+|.+.||+|++.|+.-+-.. +.||-||+++.++
T Consensus 485 Glri~F~dGsR~VfRLSGTGSsGATiRLYie~ye~d 520 (558)
T KOG0625|consen 485 GLRIVFEDGSRIVFRLSGTGSSGATIRLYIESYEKD 520 (558)
T ss_pred ceEEEEcCCcEEEEEeccCCCCCceEEEehhhhccc
Confidence 5899999999999999977665 4678888887554
No 87
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=20.71 E-value=1.2e+02 Score=21.88 Aligned_cols=27 Identities=19% Similarity=0.266 Sum_probs=23.4
Q ss_pred cCCCCEEEEecCCCCCHHHHHHHHHhh
Q 022009 237 LADGTRLIAHFNLHHTISDIHSFIDAS 263 (304)
Q Consensus 237 l~dG~rl~~rFn~s~TV~dvr~fv~~~ 263 (304)
|+.|..+.+..+...++.||..|+...
T Consensus 24 l~~G~~l~v~~d~~~~~~di~~~~~~~ 50 (70)
T PF01206_consen 24 LPPGEVLEVLVDDPAAVEDIPRWCEEN 50 (70)
T ss_dssp SGTT-EEEEEESSTTHHHHHHHHHHHH
T ss_pred cCCCCEEEEEECCccHHHHHHHHHHHC
Confidence 567899999999999999999999876
No 88
>PF07872 DUF1659: Protein of unknown function (DUF1659); InterPro: IPR012454 This family consists of hypothetical bacterial proteins of unknown function
Probab=20.35 E-value=1.2e+02 Score=20.85 Aligned_cols=31 Identities=19% Similarity=0.281 Sum_probs=21.4
Q ss_pred ceeEEEEcCCCC-----E--EEEec---CCCCCHHHHHHHH
Q 022009 230 STSVQIRLADGT-----R--LIAHF---NLHHTISDIHSFI 260 (304)
Q Consensus 230 ~t~IqIRl~dG~-----r--l~~rF---n~s~TV~dvr~fv 260 (304)
.++|+||+-+|. - ...+| ..+.|-.|||+-.
T Consensus 5 ~s~L~l~~~~G~d~~Gkpi~k~ks~~nvk~~Atdedl~~Va 45 (47)
T PF07872_consen 5 SSSLRLKYQTGVDENGKPIFKTKSFSNVKPDATDEDLYDVA 45 (47)
T ss_pred ceEEEEEEEcccCCCCCEEEEeeehhhcCCCCCHHHHHHHh
Confidence 468899997763 2 23444 4789999998753
Done!