Query psy7979
Match_columns 186
No_of_seqs 126 out of 242
Neff 6.2
Searched_HMMs 46136
Date Fri Aug 16 23:43:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7979.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7979hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2660|consensus 100.0 9.6E-45 2.1E-49 313.5 9.7 170 9-182 48-234 (331)
2 PF11816 DUF3337: Domain of un 98.3 5.5E-06 1.2E-10 73.3 9.7 90 92-182 213-329 (331)
3 cd01612 APG12_C Ubiquitin-like 97.6 0.00096 2.1E-08 48.4 9.3 82 94-183 2-84 (87)
4 cd01611 GABARAP Ubiquitin doma 97.3 0.0032 7E-08 47.7 9.9 87 91-183 22-109 (112)
5 PF02991 Atg8: Autophagy prote 97.2 0.0074 1.6E-07 45.2 10.7 84 92-181 15-99 (104)
6 PTZ00380 microtubule-associate 97.2 0.0032 6.9E-08 48.5 8.8 80 92-180 26-105 (121)
7 KOG1654|consensus 96.1 0.047 1E-06 41.4 8.1 83 93-180 28-110 (116)
8 PF00240 ubiquitin: Ubiquitin 95.9 0.018 3.8E-07 38.7 4.8 46 115-163 9-54 (69)
9 smart00213 UBQ Ubiquitin homol 95.9 0.027 5.8E-07 36.7 5.4 46 115-163 13-58 (64)
10 PF13764 E3_UbLigase_R4: E3 ub 95.6 0.025 5.4E-07 55.7 6.0 58 123-182 16-79 (802)
11 cd01798 parkin_N amino-termina 95.5 0.036 7.9E-07 37.7 5.1 46 115-163 12-57 (70)
12 cd01815 BMSC_UbP_N Ubiquitin-l 95.3 0.03 6.6E-07 39.6 4.2 45 119-163 18-62 (75)
13 PF04110 APG12: Ubiquitin-like 95.3 0.11 2.5E-06 37.7 7.3 82 94-183 2-84 (87)
14 cd01805 RAD23_N Ubiquitin-like 95.1 0.069 1.5E-06 36.6 5.4 46 115-163 14-61 (77)
15 cd01794 DC_UbP_C dendritic cel 95.0 0.062 1.4E-06 37.0 5.0 46 114-162 11-56 (70)
16 cd01796 DDI1_N DNA damage indu 94.8 0.069 1.5E-06 36.7 4.8 46 115-163 13-59 (71)
17 cd01807 GDX_N ubiquitin-like d 94.7 0.089 1.9E-06 36.2 5.2 45 116-163 15-59 (74)
18 cd01769 UBL Ubiquitin-like dom 94.4 0.11 2.4E-06 34.2 4.9 45 115-162 11-55 (69)
19 cd01810 ISG15_repeat2 ISG15 ub 94.2 0.14 3E-06 35.2 5.3 44 116-162 13-56 (74)
20 cd01806 Nedd8 Nebb8-like ubiq 94.1 0.16 3.4E-06 34.4 5.4 45 116-163 15-59 (76)
21 cd01803 Ubiquitin Ubiquitin. U 93.9 0.16 3.4E-06 34.4 5.1 45 116-163 15-59 (76)
22 cd01791 Ubl5 UBL5 ubiquitin-li 93.9 0.14 3E-06 35.6 4.8 58 115-179 15-72 (73)
23 cd01793 Fubi Fubi ubiquitin-li 93.9 0.17 3.7E-06 34.8 5.1 46 114-162 11-56 (74)
24 cd01809 Scythe_N Ubiquitin-lik 93.8 0.19 4.2E-06 33.6 5.3 46 115-163 14-59 (72)
25 cd01808 hPLIC_N Ubiquitin-like 93.5 0.21 4.6E-06 34.0 5.1 45 116-163 14-58 (71)
26 KOG0311|consensus 93.5 0.043 9.3E-07 49.2 1.9 42 8-52 76-117 (381)
27 PTZ00044 ubiquitin; Provisiona 93.5 0.22 4.8E-06 34.0 5.1 46 115-163 14-59 (76)
28 cd01804 midnolin_N Ubiquitin-l 93.3 0.19 4.1E-06 35.2 4.6 46 114-163 14-59 (78)
29 cd01812 BAG1_N Ubiquitin-like 93.3 0.18 4E-06 33.8 4.5 45 116-163 14-58 (71)
30 PF11976 Rad60-SLD: Ubiquitin- 93.0 0.37 8E-06 32.6 5.6 50 113-164 12-61 (72)
31 cd01802 AN1_N ubiquitin-like d 92.5 0.34 7.3E-06 36.0 5.2 47 114-163 40-86 (103)
32 cd01790 Herp_N Homocysteine-re 90.3 0.68 1.5E-05 33.0 4.7 61 116-179 18-78 (79)
33 PF13881 Rad60-SLD_2: Ubiquiti 89.8 0.59 1.3E-05 35.3 4.3 54 114-167 16-73 (111)
34 cd01797 NIRF_N amino-terminal 89.6 0.78 1.7E-05 32.1 4.5 43 118-163 19-61 (78)
35 cd01763 Sumo Small ubiquitin-r 88.9 4.1 8.9E-05 28.9 8.0 62 91-163 9-70 (87)
36 cd01792 ISG15_repeat1 ISG15 ub 88.5 0.8 1.7E-05 31.9 4.0 46 115-163 16-63 (80)
37 cd01800 SF3a120_C Ubiquitin-li 88.5 1.4 3E-05 30.4 5.1 46 116-164 12-57 (76)
38 KOG0308|consensus 88.0 0.29 6.2E-06 47.1 1.8 41 143-184 667-721 (735)
39 cd00196 UBQ Ubiquitin-like pro 86.3 2.3 5E-05 25.4 4.8 45 113-160 9-53 (69)
40 cd01795 USP48_C USP ubiquitin- 85.2 1.9 4.1E-05 32.4 4.5 44 115-161 18-62 (107)
41 cd01799 Hoil1_N Ubiquitin-like 84.7 4.4 9.6E-05 28.2 6.1 45 115-163 16-61 (75)
42 cd01813 UBP_N UBP ubiquitin pr 83.8 2.4 5.1E-05 29.4 4.3 46 116-164 14-62 (74)
43 PF10302 DUF2407: DUF2407 ubiq 82.4 2.2 4.8E-05 31.4 3.9 45 118-163 20-64 (97)
44 KOG3439|consensus 80.5 23 0.0005 27.0 8.8 83 93-183 30-113 (116)
45 PF13878 zf-C2H2_3: zinc-finge 76.6 1.5 3.3E-05 27.2 1.3 25 2-26 4-28 (41)
46 TIGR00601 rad23 UV excision re 76.1 5.6 0.00012 36.1 5.3 46 115-163 14-62 (378)
47 cd01814 NTGP5 Ubiquitin-like N 67.9 9.6 0.00021 29.0 4.1 48 117-164 21-72 (113)
48 cd01788 ElonginB Ubiquitin-lik 67.6 11 0.00024 28.9 4.3 65 113-180 13-80 (119)
49 cd06406 PB1_P67 A PB1 domain i 67.0 22 0.00048 25.4 5.5 60 115-180 14-78 (80)
50 PF00564 PB1: PB1 domain; Int 63.1 45 0.00097 22.6 7.0 62 115-179 15-81 (84)
51 cd01775 CYR1_RA Ubiquitin doma 60.9 28 0.00061 25.8 5.3 38 114-151 15-52 (97)
52 PF10571 UPF0547: Uncharacteri 60.9 4.2 9.1E-05 22.9 0.8 11 12-22 1-11 (26)
53 cd01801 Tsc13_N Ubiquitin-like 60.7 21 0.00045 24.5 4.5 43 119-163 20-64 (77)
54 KOG0010|consensus 60.7 10 0.00023 35.6 3.7 47 113-162 26-72 (493)
55 PF03119 DNA_ligase_ZBD: NAD-d 60.7 3.5 7.5E-05 23.5 0.4 11 13-23 1-11 (28)
56 PF13240 zinc_ribbon_2: zinc-r 55.9 5.3 0.00012 21.7 0.6 13 8-20 10-22 (23)
57 cd01789 Alp11_N Ubiquitin-like 55.8 31 0.00066 24.3 4.7 35 116-152 17-51 (84)
58 PF13248 zf-ribbon_3: zinc-rib 52.9 6.3 0.00014 21.8 0.6 10 10-19 15-24 (26)
59 PF14353 CpXC: CpXC protein 52.0 7.3 0.00016 29.4 1.0 48 11-63 38-85 (128)
60 PF13842 Tnp_zf-ribbon_2: DDE_ 50.8 7.5 0.00016 22.8 0.7 20 4-23 9-28 (32)
61 COG1998 RPS31 Ribosomal protei 49.1 7.5 0.00016 25.4 0.6 17 3-19 11-27 (51)
62 PF14835 zf-RING_6: zf-RING of 47.2 14 0.0003 25.5 1.7 25 12-40 41-65 (65)
63 PRK13130 H/ACA RNA-protein com 46.7 11 0.00024 25.1 1.1 24 11-35 17-40 (56)
64 PF14803 Nudix_N_2: Nudix N-te 46.3 7.7 0.00017 23.2 0.3 15 12-26 1-15 (34)
65 PF09889 DUF2116: Uncharacteri 46.3 11 0.00024 25.4 1.1 13 9-21 1-13 (59)
66 smart00734 ZnF_Rad18 Rad18-lik 45.8 9.5 0.00021 21.3 0.6 9 13-21 3-11 (26)
67 cd06411 PB1_p51 The PB1 domain 45.3 1.1E+02 0.0024 21.8 6.4 59 116-180 11-76 (78)
68 PF05080 DUF681: Protein of un 44.1 3.3 7.1E-05 30.0 -1.8 25 115-140 74-98 (101)
69 KOG3493|consensus 43.8 3.9 8.5E-05 28.4 -1.4 49 112-163 12-60 (73)
70 TIGR01682 moaD molybdopterin c 43.5 40 0.00087 23.1 3.7 46 115-161 19-66 (80)
71 cd06407 PB1_NLP A PB1 domain i 42.1 42 0.00091 23.8 3.6 62 114-178 12-79 (82)
72 KOG0006|consensus 41.4 32 0.00069 31.0 3.5 40 119-161 21-60 (446)
73 PRK00432 30S ribosomal protein 38.9 13 0.00028 24.0 0.5 17 3-19 12-28 (50)
74 PF09237 GAGA: GAGA factor; I 38.5 8.9 0.00019 25.4 -0.3 12 12-23 25-36 (54)
75 PF08154 NLE: NLE (NUC135) dom 38.4 1.1E+02 0.0023 20.5 5.0 45 111-156 15-59 (65)
76 smart00504 Ubox Modified RING 35.8 27 0.00059 22.4 1.7 27 11-41 35-61 (63)
77 PF06677 Auto_anti-p27: Sjogre 34.6 18 0.0004 22.5 0.7 12 10-21 16-27 (41)
78 PF14560 Ubiquitin_2: Ubiquiti 33.9 1.1E+02 0.0024 21.2 4.7 27 116-144 18-44 (87)
79 PF00788 RA: Ras association ( 33.6 1.5E+02 0.0033 20.0 8.6 70 112-184 17-93 (93)
80 PF13453 zf-TFIIB: Transcripti 33.2 15 0.00033 22.3 0.2 10 13-22 1-10 (41)
81 COG3809 Uncharacterized protei 31.8 19 0.00042 25.9 0.5 22 13-35 3-24 (88)
82 PLN02560 enoyl-CoA reductase 31.6 96 0.0021 27.4 4.9 47 115-163 17-70 (308)
83 PF10407 Cytokin_check_N: Cdc1 31.1 81 0.0018 22.1 3.5 52 113-164 3-59 (73)
84 cd06408 PB1_NoxR The PB1 domai 30.1 1.2E+02 0.0026 21.9 4.4 43 112-160 12-54 (86)
85 PF09379 FERM_N: FERM N-termin 29.0 1.5E+02 0.0033 19.7 4.7 64 113-182 8-77 (80)
86 PF10601 zf-LITAF-like: LITAF- 28.5 23 0.0005 24.1 0.4 16 7-22 54-69 (73)
87 smart00714 LITAF Possible memb 28.5 25 0.00055 23.5 0.6 17 6-22 47-63 (67)
88 PF09151 DUF1936: Domain of un 28.2 26 0.00057 20.8 0.6 10 12-21 2-11 (36)
89 PF07797 DUF1639: Protein of u 27.8 38 0.00083 22.1 1.3 23 30-52 23-45 (50)
90 PF02597 ThiS: ThiS family; I 27.8 45 0.00097 22.1 1.8 47 113-160 13-62 (77)
91 PF11324 DUF3126: Protein of u 27.5 1.2E+02 0.0025 20.8 3.7 32 124-155 2-40 (63)
92 PF13920 zf-C3HC4_3: Zinc fing 27.4 34 0.00074 21.3 1.1 13 10-22 36-48 (50)
93 PF07282 OrfB_Zn_ribbon: Putat 27.1 36 0.00079 22.6 1.2 17 7-23 24-40 (69)
94 PF04423 Rad50_zn_hook: Rad50 27.0 23 0.0005 22.7 0.2 10 13-22 22-31 (54)
95 KOG4248|consensus 26.8 81 0.0017 32.6 4.0 46 114-162 15-60 (1143)
96 PF14451 Ub-Mut7C: Mut7-C ubiq 26.8 73 0.0016 22.6 2.8 40 115-161 26-66 (81)
97 cd01770 p47_UBX p47-like ubiqu 26.6 2.2E+02 0.0048 19.7 5.3 50 112-163 15-67 (79)
98 COG1885 Uncharacterized protei 26.6 32 0.00069 26.0 0.9 33 6-42 44-76 (115)
99 COG2260 Predicted Zn-ribbon RN 26.4 36 0.00077 23.0 1.0 16 12-27 18-33 (59)
100 PF10588 NADH-G_4Fe-4S_3: NADH 26.2 51 0.0011 20.2 1.6 22 11-43 13-34 (41)
101 PF04564 U-box: U-box domain; 25.9 51 0.0011 22.4 1.8 29 10-42 38-66 (73)
102 PF11620 GABP-alpha: GA-bindin 25.9 67 0.0015 23.4 2.4 40 120-162 11-50 (88)
103 COG3716 ManZ Phosphotransferas 25.7 30 0.00064 30.2 0.7 18 33-50 216-233 (269)
104 PF15044 CLU_N: Mitochondrial 25.3 1.1E+02 0.0025 21.1 3.5 44 119-164 2-45 (76)
105 cd00754 MoaD Ubiquitin domain 25.1 1.1E+02 0.0024 20.3 3.5 45 116-160 20-65 (80)
106 PF13824 zf-Mss51: Zinc-finger 25.1 45 0.00097 22.2 1.3 19 8-26 11-29 (55)
107 TIGR00599 rad18 DNA repair pro 24.3 53 0.0011 30.2 2.0 28 12-43 61-88 (397)
108 smart00661 RPOL9 RNA polymeras 23.2 40 0.00086 21.0 0.8 11 12-22 1-11 (52)
109 KOG3109|consensus 23.2 43 0.00094 28.7 1.2 25 19-43 88-112 (244)
110 PF10367 Vps39_2: Vacuolar sor 22.9 48 0.001 23.4 1.2 24 9-34 76-99 (109)
111 COG0267 RpmG Ribosomal protein 22.4 30 0.00066 22.6 0.1 16 6-21 29-44 (50)
112 COG1645 Uncharacterized Zn-fin 22.3 32 0.0007 26.8 0.2 12 10-21 27-38 (131)
113 cd00350 rubredoxin_like Rubred 22.2 55 0.0012 19.0 1.2 11 10-20 16-26 (33)
114 PF09297 zf-NADH-PPase: NADH p 22.1 48 0.001 19.0 0.9 13 10-22 2-14 (32)
115 smart00295 B41 Band 4.1 homolo 21.7 3.9E+02 0.0084 20.7 6.7 63 113-182 15-83 (207)
116 smart00746 TRASH metallochaper 21.5 48 0.001 17.5 0.8 9 14-22 1-9 (39)
117 PF02150 RNA_POL_M_15KD: RNA p 21.4 39 0.00085 20.1 0.4 11 12-22 2-12 (35)
118 COG4068 Uncharacterized protei 20.8 51 0.0011 22.4 0.9 38 10-59 7-44 (64)
119 PF08783 DWNN: DWNN domain; I 20.4 1.5E+02 0.0033 20.7 3.3 28 120-149 19-46 (74)
120 KOG2015|consensus 20.2 75 0.0016 29.0 2.1 34 9-46 326-359 (422)
121 PRK00420 hypothetical protein; 20.2 48 0.001 25.2 0.8 16 8-23 37-52 (112)
122 PRK00418 DNA gyrase inhibitor; 20.0 73 0.0016 21.7 1.6 12 10-21 5-16 (62)
No 1
>KOG2660|consensus
Probab=100.00 E-value=9.6e-45 Score=313.47 Aligned_cols=170 Identities=49% Similarity=0.793 Sum_probs=140.0
Q ss_pred cCCCCCCcccccccccCCccccccchhHHhhhHhhcccchhhHHHHHHHHHHHhC-CCCCCCCCCC------chhhhccc
Q psy7979 9 KIKNTCPSCNIIIHQSHPLQYISFDRTMQDLVYKLVPNLQANEMKREREFYRIRG-LPCPKDLLLE------DEEEENTD 81 (186)
Q Consensus 9 ~~~~~CP~C~~~ih~s~Pl~~i~~D~tLQdIVyKLVPgL~~~E~~rr~eFy~~~~-~~~p~~~~~~------~~~~~~~~ 81 (186)
+.+++||+|++.||+++|++||++|+|||||||||||||+++|++++++||+++| +..|++.... .++...+.
T Consensus 48 ~~~~~CP~C~i~ih~t~pl~ni~~DrtlqdiVyKLVPgl~erE~k~~rdFy~~~~~~d~~~~~~~~~~~~~~~ek~~~t~ 127 (331)
T KOG2660|consen 48 EESKYCPTCDIVIHKTHPLLNIRSDRTLQDIVYKLVPGLQEREMKRRRDFYKSRPLVDVPAGDTPERGHVLGEEKVPDTS 127 (331)
T ss_pred HHhccCCccceeccCccccccCCcchHHHHHHHHHcchHHHHHHHHHHHHHHhCCCcccCCCCCcccccccCcccCCCch
Confidence 4589999999999999999999999999999999999999999999999999999 6666554321 11100000
Q ss_pred ---------cccCCCCCCCCceeEEEEeccCCCCccccccccEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCE
Q psy7979 82 ---------QVNSDYHRLDEQVNVYLECSVATTSSLKTLKKRFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDE 152 (186)
Q Consensus 82 ---------~~~~~~~~~de~vsl~LE~~~~~~~~l~~l~~~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~ 152 (186)
..+...|+.|+++++.++.. .++++.+.++|+||||++||+||+|||+.|+++ ++...+|||+|+++
T Consensus 128 ~~~~s~~l~~~~~~~~r~d~~~~~~~~e~---~~~~k~l~~~fvrcsa~~Tv~hlkkfl~~k~~~-~~~~~~idi~~~d~ 203 (331)
T KOG2660|consen 128 DEIASLSLEVEDFKQNRLDEQVSVGLDEG---KDTLKDLVRRFLRCSAAATVNHLKKFLRKKMDN-LSNKSEIDILCEEE 203 (331)
T ss_pred hhhhccccchhhcccchhhhhhhcCCCcc---cccccccccceEeccHHHHHHHHHHHHHHHhcc-ccchhhheeecCCc
Confidence 01123456677777766544 567888889999999999999999999999953 88899999999999
Q ss_pred ecCCCCcHHHH-HHHhccCCCCCeeEEEeec
Q psy7979 153 LLGKDHTLKFV-YITRWRFRTPPLKLQYRPR 182 (186)
Q Consensus 153 ~L~~~~TL~~I-~~~~W~~~~~Pm~L~Yr~~ 182 (186)
+|++++||++| +.++|+.+++||+|+||..
T Consensus 204 ~l~~~~TLk~i~~~~~~~~r~~pL~l~y~v~ 234 (331)
T KOG2660|consen 204 LLGDYYTLKDIAYAYRWRSRDPPLPLRYRVK 234 (331)
T ss_pred cccchhhhhhhhhhhcccccCCcceeEeccc
Confidence 99999999987 7778875799999999954
No 2
>PF11816 DUF3337: Domain of unknown function (DUF3337); InterPro: IPR021772 This family of proteins are functionally uncharacterised. This family is only found in eukaryotes. This presumed domain is typically between 285 to 342 amino acids in length.
Probab=98.27 E-value=5.5e-06 Score=73.25 Aligned_cols=90 Identities=23% Similarity=0.346 Sum_probs=66.2
Q ss_pred CceeEEEEeccCCCC-------------ccccccccEEEe--cccccHHHHHHHHHHHhh----c--------CCCCCce
Q psy7979 92 EQVNVYLECSVATTS-------------SLKTLKKRFIRL--SSQATITHLKKFVALKLL----D--------EKSKYKE 144 (186)
Q Consensus 92 e~vsl~LE~~~~~~~-------------~l~~l~~~ylrc--s~~~tV~hLkKfL~~Kl~----~--------~l~~~~~ 144 (186)
.-|+|.|........ .++.+..--.|. +..+.|.=+.-||+.|+. . .+..+.-
T Consensus 213 ~Ki~F~L~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rL~A~~mLrvkKI~~yV~ek~~~~~~~~~~~~~~~~~~p~e~ 292 (331)
T PF11816_consen 213 PKISFVLQPWDGSLPPNLKPDGKSQKKIKLPPLSEGNSRLNAPRMLRVKKILEYVAEKLEKTPESKTPEMKPKKLKPEEW 292 (331)
T ss_pred CeeEEEEeecCCCCccccCCCccccccccccccccccceecccchhhhHHHHHHHHHHhccCccccCccccccCCCCCce
Confidence 348999977641110 022222233444 678999999999999991 0 1123457
Q ss_pred EEEEeCCEecCCCCcHHHHHHHhccCCCCCeeEEEeec
Q psy7979 145 IDILCNDELLGKDHTLKFVYITRWRFRTPPLKLQYRPR 182 (186)
Q Consensus 145 veIlc~~~~L~~~~TL~~I~~~~W~~~~~Pm~L~Yr~~ 182 (186)
+||+|+|++|+.++||.-|.-+.||. .+-|+|+||.+
T Consensus 293 lEl~C~gqvL~~~mtLaTVr~~~WK~-~~di~L~YR~k 329 (331)
T PF11816_consen 293 LELLCNGQVLPPDMTLATVRTFIWKS-SGDIVLHYRRK 329 (331)
T ss_pred EEEEeCCeEcCCcCCHHHHHHhhccC-CCeEEEEEEec
Confidence 99999999999999999999999996 78999999986
No 3
>cd01612 APG12_C Ubiquitin-like domain of APG12. APG12_C The carboxy-terminal ubiquitin-like domain of APG12. Autophagy is a process in which cytoplasmic components are delivered to the lysosome/vacuole for degradation. Autophagy requires a ubiquitin-like protein conjugation system, in which APG12 is covalently bound to APG5.
Probab=97.57 E-value=0.00096 Score=48.41 Aligned_cols=82 Identities=15% Similarity=0.236 Sum_probs=65.1
Q ss_pred eeEEEEeccCCCCccccccccEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecC-CCCcHHHHHHHhccCCC
Q psy7979 94 VNVYLECSVATTSSLKTLKKRFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLG-KDHTLKFVYITRWRFRT 172 (186)
Q Consensus 94 vsl~LE~~~~~~~~l~~l~~~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~-~~~TL~~I~~~~W~~~~ 172 (186)
|.+.|-.. ++++.+.++=..+|+..||+.+.+||+++| ++++...|=+++|+..++ .+.||.++|..+ . .+
T Consensus 2 v~i~~~~~----g~~p~l~k~kflv~~~~tv~~~~~~lrk~L--~l~~~~slflyvnn~f~p~~d~~~g~LY~~~-~-~d 73 (87)
T cd01612 2 VTIRFKPI----GSAPILKQKVFKISATQSFQAVIDFLRKRL--KLKASDSLFLYINNSFAPSPDENVGNLYRCF-G-TN 73 (87)
T ss_pred eEEEEEEC----CCCccccccEEEeCCCCCHHHHHHHHHHHh--CCCccCeEEEEECCccCCCchhHHHHHHHhc-C-CC
Confidence 45555443 357888877777999999999999999999 888887788889886344 568999999888 5 48
Q ss_pred CCeeEEEeecc
Q psy7979 173 PPLKLQYRPRI 183 (186)
Q Consensus 173 ~Pm~L~Yr~~~ 183 (186)
+-|.+.|.-..
T Consensus 74 GfLyi~Ys~~~ 84 (87)
T cd01612 74 GELIVSYCKTV 84 (87)
T ss_pred CEEEEEEeCcc
Confidence 99999997543
No 4
>cd01611 GABARAP Ubiquitin domain of GABA-receptor-associated protein. GABARAP (GABA-receptor-associated protein) belongs ot a large family of proteins that mediate intracellular membrane trafficking and/or fusion. GABARAP binds not only to GABA, type A but also to tubulin, gephrin, and ULK1. Orthologues of GABARAP include Gate-16 (golgi-associated ATPase enhancer), LC3 (microtubule-associated protein light chain 3), and ATG8 (autophagy protein 8). ATG8 is a ubiquitin-like protein that is conjugated to the membrane phospholipid, phosphatidylethanolamine as part of a ubiquitin-like conjugation system essential for autophagosome-formation.
Probab=97.33 E-value=0.0032 Score=47.71 Aligned_cols=87 Identities=17% Similarity=0.261 Sum_probs=69.9
Q ss_pred CCceeEEEEeccCCCCccccccc-cEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHHHHHhcc
Q psy7979 91 DEQVNVYLECSVATTSSLKTLKK-RFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFVYITRWR 169 (186)
Q Consensus 91 de~vsl~LE~~~~~~~~l~~l~~-~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I~~~~W~ 169 (186)
.+.|-+.+|..+ .++++.+.+ +|+ +|+.+||+++..+|+++| .+++...+=++||+...+.+.||.++|..+-.
T Consensus 22 p~~iPVIvE~~~--~~~~p~l~k~Kfl-Vp~~~tv~~f~~~irk~l--~l~~~~slfl~Vn~~~p~~~~~~~~lY~~~kd 96 (112)
T cd01611 22 PDRIPVIVERYP--KSDLPDLDKKKYL-VPSDLTVGQFVYIIRKRI--QLRPEKALFLFVNNSLPPTSATMSQLYEEHKD 96 (112)
T ss_pred CCceEEEEEEcC--CCCcccccCceEE-ecCCCCHHHHHHHHHHHh--CCCccceEEEEECCccCCchhHHHHHHHHhCC
Confidence 346888888763 345666654 565 999999999999999999 88888788899999777788889999977665
Q ss_pred CCCCCeeEEEeecc
Q psy7979 170 FRTPPLKLQYRPRI 183 (186)
Q Consensus 170 ~~~~Pm~L~Yr~~~ 183 (186)
.++-|-|.|+-..
T Consensus 97 -~DGfLyl~Ys~~~ 109 (112)
T cd01611 97 -EDGFLYMTYSSEE 109 (112)
T ss_pred -CCCEEEEEEeccc
Confidence 3889999997543
No 5
>PF02991 Atg8: Autophagy protein Atg8 ubiquitin like; InterPro: IPR004241 Autophagy is generally known as a process involved in the degradation of bulk cytoplasmic components that are non-specifically sequestered into an autophagosome, where they are sequestered into double-membrane vesicles and delivered to the degradative organelle, the lysosome/vacuole, for breakdown and eventual recycling of the resulting macromolecules. The yeast proteins are involved in the autophagosome, and Atg8 binds Atg19, via its N terminus and the C terminus of Atg19. Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity [] Related proteins that belong to this group include the human ganglioside expression factor and a symbiosis-related fungal protein.; PDB: 3ECI_A 3D32_B 1GNU_A 1KM7_A 1KLV_A 1KOT_A 3DOW_A 1KJT_A 1V49_A 2ZJD_C ....
Probab=97.21 E-value=0.0074 Score=45.22 Aligned_cols=84 Identities=19% Similarity=0.277 Sum_probs=63.7
Q ss_pred CceeEEEEeccCCCCccccccc-cEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHHHHHhccC
Q psy7979 92 EQVNVYLECSVATTSSLKTLKK-RFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFVYITRWRF 170 (186)
Q Consensus 92 e~vsl~LE~~~~~~~~l~~l~~-~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I~~~~W~~ 170 (186)
+.|-+.+|..+ .+.++.+.+ +|| +|..+||+++...|+.++ .+++..-+=+++||...+.+.||.+||..+-.
T Consensus 15 ~~IPVIvEr~~--~s~lp~ldk~KfL-vp~~~tv~qf~~~ir~rl--~l~~~~alfl~Vn~~lp~~s~tm~elY~~~kd- 88 (104)
T PF02991_consen 15 DKIPVIVERYP--KSKLPDLDKKKFL-VPKDLTVGQFVYIIRKRL--QLSPEQALFLFVNNTLPSTSSTMGELYEKYKD- 88 (104)
T ss_dssp TEEEEEEEE-T--TSSS---SSSEEE-EETTSBHHHHHHHHHHHT--T--TTS-EEEEBTTBESSTTSBHHHHHHHHB--
T ss_pred CccEEEEEEcc--CCChhhcCccEEE-EcCCCchhhHHHHhhhhh--cCCCCceEEEEEcCcccchhhHHHHHHHHhCC-
Confidence 46888888764 334777765 455 899999999999999999 89888888899999888889999999987765
Q ss_pred CCCCeeEEEee
Q psy7979 171 RTPPLKLQYRP 181 (186)
Q Consensus 171 ~~~Pm~L~Yr~ 181 (186)
.++-|-+.|.-
T Consensus 89 eDGFLY~~Ys~ 99 (104)
T PF02991_consen 89 EDGFLYMTYSS 99 (104)
T ss_dssp TTSSEEEEEES
T ss_pred CCCeEEEEecc
Confidence 48999999964
No 6
>PTZ00380 microtubule-associated protein (MAP); Provisional
Probab=97.20 E-value=0.0032 Score=48.46 Aligned_cols=80 Identities=21% Similarity=0.156 Sum_probs=66.0
Q ss_pred CceeEEEEeccCCCCccccccccEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHHHHHhccCC
Q psy7979 92 EQVNVYLECSVATTSSLKTLKKRFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFVYITRWRFR 171 (186)
Q Consensus 92 e~vsl~LE~~~~~~~~l~~l~~~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I~~~~W~~~ 171 (186)
+.|-+.+|..+. +. .+++|+-+|..+||+.+...|++++ +|++.. +=+++||..++.+.||-+||..+-..
T Consensus 26 drIPVIvEk~~~--s~---dK~KfllVP~d~tV~qF~~iIRkrl--~l~~~k-~flfVnn~lp~~s~~mg~lYe~~KDe- 96 (121)
T PTZ00380 26 GHVAVVVEAAEK--AG---SKVHFLALPRDATVAELEAAVRQAL--GTSAKK-VTLAIEGSTPAVTATVGDIADACKRD- 96 (121)
T ss_pred CccEEEEeecCC--CC---CceEEEEcCCCCcHHHHHHHHHHHc--CCChhH-EEEEECCccCCccchHHHHHHHhcCC-
Confidence 468888887532 11 5778999999999999999999999 899886 88889998788888899999877664
Q ss_pred CCCeeEEEe
Q psy7979 172 TPPLKLQYR 180 (186)
Q Consensus 172 ~~Pm~L~Yr 180 (186)
++-|=+.|+
T Consensus 97 DGFLYi~Ys 105 (121)
T PTZ00380 97 DGFLYVSVR 105 (121)
T ss_pred CCeEEEEEc
Confidence 888888885
No 7
>KOG1654|consensus
Probab=96.13 E-value=0.047 Score=41.40 Aligned_cols=83 Identities=18% Similarity=0.200 Sum_probs=65.7
Q ss_pred ceeEEEEeccCCCCccccccccEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHHHHHhccCCC
Q psy7979 93 QVNVYLECSVATTSSLKTLKKRFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFVYITRWRFRT 172 (186)
Q Consensus 93 ~vsl~LE~~~~~~~~l~~l~~~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I~~~~W~~~~ 172 (186)
-|-+..|+. +...++.+.++=.-+|+.+||+++-+.|++++ .|+.+.-+=++.||...+...+|-.||...-.. +
T Consensus 28 riPVIvEk~--~~~~lp~lDK~KyLVP~dltvgqfi~iIRkRi--qL~~~kA~flfVn~~~p~ts~~ms~~Ye~~kde-D 102 (116)
T KOG1654|consen 28 RIPVIVEKA--GKSQLPDLDKKKYLVPDDLTVGQFIKIIRKRI--QLSPEKAFFLFVNNTSPPTSATMSALYEEEKDE-D 102 (116)
T ss_pred CCcEEEEec--ccccCcccccceeeccccccHHHHHHHHHHHh--ccChhHeEEEEEcCcCCcchhhHHHHHHhhccc-C
Confidence 356667754 34568888886666899999999999999999 999998898999997777766666789877654 6
Q ss_pred CCeeEEEe
Q psy7979 173 PPLKLQYR 180 (186)
Q Consensus 173 ~Pm~L~Yr 180 (186)
+-|=+.|+
T Consensus 103 gFLYm~Ys 110 (116)
T KOG1654|consen 103 GFLYMTYS 110 (116)
T ss_pred cEEEEEec
Confidence 77777664
No 8
>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=95.94 E-value=0.018 Score=38.75 Aligned_cols=46 Identities=20% Similarity=0.226 Sum_probs=40.3
Q ss_pred EEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHH
Q psy7979 115 FIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFV 163 (186)
Q Consensus 115 ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I 163 (186)
-+.++...||..||+.|+.+. +++.. ++-++|+|..|.++.||.+.
T Consensus 9 ~~~v~~~~tV~~lK~~i~~~~--~~~~~-~~~L~~~G~~L~d~~tL~~~ 54 (69)
T PF00240_consen 9 TLEVDPDDTVADLKQKIAEET--GIPPE-QQRLIYNGKELDDDKTLSDY 54 (69)
T ss_dssp EEEEETTSBHHHHHHHHHHHH--TSTGG-GEEEEETTEEESTTSBTGGG
T ss_pred EEEECCCCCHHHhhhhccccc--ccccc-cceeeeeeecccCcCcHHHc
Confidence 577889999999999999999 77754 67799999999999999764
No 9
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=95.89 E-value=0.027 Score=36.70 Aligned_cols=46 Identities=17% Similarity=0.192 Sum_probs=39.9
Q ss_pred EEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHH
Q psy7979 115 FIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFV 163 (186)
Q Consensus 115 ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I 163 (186)
-+.+++..||..||.-|+.++ +++.. ++-++|+|..|.++.||.+.
T Consensus 13 ~~~v~~~~tv~~lk~~i~~~~--~~~~~-~~~L~~~g~~L~d~~tL~~~ 58 (64)
T smart00213 13 TLEVKPSDTVSELKEKIAELT--GIPVE-QQRLIYKGKVLEDDRTLADY 58 (64)
T ss_pred EEEECCCCcHHHHHHHHHHHH--CCCHH-HEEEEECCEECCCCCCHHHc
Confidence 477889999999999999999 77754 67789999999999999764
No 10
>PF13764 E3_UbLigase_R4: E3 ubiquitin-protein ligase UBR4
Probab=95.58 E-value=0.025 Score=55.70 Aligned_cols=58 Identities=24% Similarity=0.521 Sum_probs=51.8
Q ss_pred cHHHHHHHHHHHhhcCCCC----CceEEEEeCCEecCCCCcHHHHHHHhccC--CCCCeeEEEeec
Q psy7979 123 TITHLKKFVALKLLDEKSK----YKEIDILCNDELLGKDHTLKFVYITRWRF--RTPPLKLQYRPR 182 (186)
Q Consensus 123 tV~hLkKfL~~Kl~~~l~~----~~~veIlc~~~~L~~~~TL~~I~~~~W~~--~~~Pm~L~Yr~~ 182 (186)
+++.+|.+|+.-+ ++.. .+-+|++++|.++.-++++.+||..-|+. ...||+..||+.
T Consensus 16 lmrdvknkIc~d~--~m~~lleDd~gmELlV~~~IisldL~v~~Vy~~vW~~~~~~~pM~v~YR~~ 79 (802)
T PF13764_consen 16 LMRDVKNKICRDL--EMIALLEDDNGMELLVNNKIISLDLPVRDVYEKVWKPNNQNPPMRVVYRMR 79 (802)
T ss_pred hHHHHHHHHhhhc--ccchhccCCcccceeecCeeecCCCcHHHHHHHHhcccCCCCCeEEEEeec
Confidence 6889999999999 7763 56799999999999999999999999984 367999999985
No 11
>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=95.52 E-value=0.036 Score=37.65 Aligned_cols=46 Identities=15% Similarity=0.226 Sum_probs=40.0
Q ss_pred EEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHH
Q psy7979 115 FIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFV 163 (186)
Q Consensus 115 ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I 163 (186)
.+.++...||..||+.|+.+. +++.. +..+.|+|.+|.++.||.+.
T Consensus 12 ~~~v~~~~tV~~lK~~i~~~~--gi~~~-~q~Li~~G~~L~d~~~l~~~ 57 (70)
T cd01798 12 PVEVDPDTDIKQLKEVVAKRQ--GVPPD-QLRVIFAGKELRNTTTIQEC 57 (70)
T ss_pred EEEECCCChHHHHHHHHHHHH--CCCHH-HeEEEECCeECCCCCcHHHc
Confidence 467788999999999999999 78754 66789999999999999873
No 12
>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=95.33 E-value=0.03 Score=39.59 Aligned_cols=45 Identities=27% Similarity=0.378 Sum_probs=38.1
Q ss_pred cccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHH
Q psy7979 119 SSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFV 163 (186)
Q Consensus 119 s~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I 163 (186)
|+..||..||.-|+.+.+.+++...+..+.|.|..|.++.||.+.
T Consensus 18 ~~~~TV~~LK~kI~~~~~egi~~~dqQrLIy~GKiL~D~~TL~dy 62 (75)
T cd01815 18 PGGYQVSTLKQLIAAQLPDSLPDPELIDLIHCGRKLKDDQTLDFY 62 (75)
T ss_pred CccCcHHHHHHHHHHhhccCCCChHHeEEEeCCcCCCCCCcHHHc
Confidence 699999999999999974456655677788999999999999874
No 13
>PF04110 APG12: Ubiquitin-like autophagy protein Apg12 ; InterPro: IPR007242 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. This entry represents Apg12, which is covalently bound to Apg5 [].; GO: 0000045 autophagic vacuole assembly, 0005737 cytoplasm; PDB: 1WZ3_B.
Probab=95.32 E-value=0.11 Score=37.72 Aligned_cols=82 Identities=20% Similarity=0.188 Sum_probs=52.9
Q ss_pred eeEEEEeccCCCCccccccccEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCC-EecCCCCcHHHHHHHhccCCC
Q psy7979 94 VNVYLECSVATTSSLKTLKKRFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCND-ELLGKDHTLKFVYITRWRFRT 172 (186)
Q Consensus 94 vsl~LE~~~~~~~~l~~l~~~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~-~~L~~~~TL~~I~~~~W~~~~ 172 (186)
|.|.|-.. + +.|.+.++-..+++.-|+.++-+||+++| .+.....+=+++|+ -.=.++.|+.++|.-.- .+
T Consensus 2 V~v~fk~i---G-~aPilk~~k~kI~~~~~f~~vi~fLrk~L--k~~~~~slFlYin~sFaPspDe~vg~L~~~f~--~~ 73 (87)
T PF04110_consen 2 VTVRFKAI---G-SAPILKQKKFKISASQTFATVIAFLRKKL--KLKPSDSLFLYINNSFAPSPDETVGDLYRCFG--TN 73 (87)
T ss_dssp EEEEEEEE---T-T----S--EEEEETTSBTHHHHHHHHHHC--T----SS-EEEEEEEE---TTSBHHHHHHHH---BT
T ss_pred EEEEEEec---C-CCccccCcEEEECCCCchHHHHHHHHHHh--CCccCCeEEEEEcCccCCCchhHHHHHHHHhC--CC
Confidence 45555544 2 46778889999999999999999999999 88777778778876 34467889999975444 36
Q ss_pred CCeeEEEeecc
Q psy7979 173 PPLKLQYRPRI 183 (186)
Q Consensus 173 ~Pm~L~Yr~~~ 183 (186)
+.|.+.|..+.
T Consensus 74 ~~Liv~Ys~t~ 84 (87)
T PF04110_consen 74 GELIVSYSKTP 84 (87)
T ss_dssp TBEEEEEESSS
T ss_pred CEEEEEEeccc
Confidence 79999998653
No 14
>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=95.07 E-value=0.069 Score=36.64 Aligned_cols=46 Identities=17% Similarity=0.243 Sum_probs=39.4
Q ss_pred EEEecccccHHHHHHHHHHHhhcCC--CCCceEEEEeCCEecCCCCcHHHH
Q psy7979 115 FIRLSSQATITHLKKFVALKLLDEK--SKYKEIDILCNDELLGKDHTLKFV 163 (186)
Q Consensus 115 ylrcs~~~tV~hLkKfL~~Kl~~~l--~~~~~veIlc~~~~L~~~~TL~~I 163 (186)
.+.+++..||..||..|+.+. ++ +. .+.-++|+|.+|.++.||.+.
T Consensus 14 ~l~v~~~~TV~~lK~~i~~~~--~i~~~~-~~q~L~~~G~~L~d~~~L~~~ 61 (77)
T cd01805 14 PIEVDPDDTVAELKEKIEEEK--GCDYPP-EQQKLIYSGKILKDDTTLEEY 61 (77)
T ss_pred EEEECCCCcHHHHHHHHHHhh--CCCCCh-hHeEEEECCEEccCCCCHHHc
Confidence 477889999999999999999 76 54 466688999999999999874
No 15
>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=95.02 E-value=0.062 Score=37.01 Aligned_cols=46 Identities=20% Similarity=0.132 Sum_probs=39.3
Q ss_pred cEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHH
Q psy7979 114 RFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKF 162 (186)
Q Consensus 114 ~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~ 162 (186)
--+-++...||..||..|+.+. +++... .-++|+|.+|.++.||.+
T Consensus 11 ~~l~v~~~~TV~~lK~~I~~~~--gi~~~~-q~Li~~G~~L~D~~~l~~ 56 (70)
T cd01794 11 VKLSVSSKDTVGQLKKQLQAAE--GVDPCC-QRWFFSGKLLTDKTRLQE 56 (70)
T ss_pred EEEEECCcChHHHHHHHHHHHh--CCCHHH-eEEEECCeECCCCCCHHH
Confidence 3467788899999999999998 888664 457799999999999987
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=94.83 E-value=0.069 Score=36.68 Aligned_cols=46 Identities=9% Similarity=0.149 Sum_probs=38.1
Q ss_pred EEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCC-CcHHHH
Q psy7979 115 FIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKD-HTLKFV 163 (186)
Q Consensus 115 ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~-~TL~~I 163 (186)
-+.++...||..||..|+.+. ++|.. +.-+.|+|.+|.++ -||.+.
T Consensus 13 ~l~v~~~~TV~~lK~~I~~~~--gip~~-~q~Li~~Gk~L~D~~~~L~~~ 59 (71)
T cd01796 13 SLDVDPDLELENFKALCEAES--GIPAS-QQQLIYNGRELVDNKRLLALY 59 (71)
T ss_pred EEEECCcCCHHHHHHHHHHHh--CCCHH-HeEEEECCeEccCCcccHHHc
Confidence 367788999999999999998 88865 44588999999887 578764
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=94.75 E-value=0.089 Score=36.15 Aligned_cols=45 Identities=22% Similarity=0.354 Sum_probs=39.4
Q ss_pred EEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHH
Q psy7979 116 IRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFV 163 (186)
Q Consensus 116 lrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I 163 (186)
+.++...||..||.-|+.+. +++.. +.-++|+|.+|.++.||.+.
T Consensus 15 l~v~~~~tV~~lK~~i~~~~--gi~~~-~q~L~~~G~~L~d~~~L~~~ 59 (74)
T cd01807 15 LQVSEKESVSTLKKLVSEHL--NVPEE-QQRLLFKGKALADDKRLSDY 59 (74)
T ss_pred EEECCCCcHHHHHHHHHHHH--CCCHH-HeEEEECCEECCCCCCHHHC
Confidence 67889999999999999999 88754 56688999999999999874
No 18
>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=94.41 E-value=0.11 Score=34.15 Aligned_cols=45 Identities=22% Similarity=0.245 Sum_probs=38.4
Q ss_pred EEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHH
Q psy7979 115 FIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKF 162 (186)
Q Consensus 115 ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~ 162 (186)
-+.++...||..||+.|+.+. +++.. .+-++++|..|.++.||.+
T Consensus 11 ~~~~~~~~ti~~lK~~i~~~~--~~~~~-~~~l~~~g~~l~d~~~l~~ 55 (69)
T cd01769 11 ELEVSPDDTVAELKAKIAAKE--GVPPE-QQRLIYAGKILKDDKTLSD 55 (69)
T ss_pred EEEECCCChHHHHHHHHHHHH--CcChH-HEEEEECCcCCCCcCCHHH
Confidence 467888999999999999999 77654 5667899999999999876
No 19
>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=94.24 E-value=0.14 Score=35.24 Aligned_cols=44 Identities=14% Similarity=0.129 Sum_probs=38.1
Q ss_pred EEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHH
Q psy7979 116 IRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKF 162 (186)
Q Consensus 116 lrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~ 162 (186)
+.++...||..||+-|+.+. +++.. +.-+.|+|.+|.++.||.+
T Consensus 13 l~v~~~~tV~~lK~~I~~~~--gi~~~-~q~L~~~G~~L~D~~tL~~ 56 (74)
T cd01810 13 YEVQLTQTVATLKQQVSQRE--RVQAD-QFWLSFEGRPMEDEHPLGE 56 (74)
T ss_pred EEECCcChHHHHHHHHHHHh--CCCHH-HeEEEECCEECCCCCCHHH
Confidence 66778899999999999998 88865 4457899999999999987
No 20
>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=94.13 E-value=0.16 Score=34.44 Aligned_cols=45 Identities=13% Similarity=0.152 Sum_probs=38.9
Q ss_pred EEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHH
Q psy7979 116 IRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFV 163 (186)
Q Consensus 116 lrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I 163 (186)
++++...||..||..|+.+. +++.. +.-+.++|..|.++.||.+.
T Consensus 15 ~~v~~~~tv~~lK~~i~~~~--g~~~~-~qrL~~~g~~L~d~~tl~~~ 59 (76)
T cd01806 15 IDIEPTDKVERIKERVEEKE--GIPPQ-QQRLIYSGKQMNDDKTAADY 59 (76)
T ss_pred EEECCCCCHHHHHHHHhHhh--CCChh-hEEEEECCeEccCCCCHHHc
Confidence 67889999999999999999 88866 45577999999999999874
No 21
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=93.95 E-value=0.16 Score=34.44 Aligned_cols=45 Identities=16% Similarity=0.127 Sum_probs=39.0
Q ss_pred EEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHH
Q psy7979 116 IRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFV 163 (186)
Q Consensus 116 lrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I 163 (186)
+.+++..||..||+.|+.+. +++.. +.-+.|+|..|.++.||.+.
T Consensus 15 ~~v~~~~tV~~lK~~i~~~~--g~~~~-~q~L~~~g~~L~d~~~L~~~ 59 (76)
T cd01803 15 LEVEPSDTIENVKAKIQDKE--GIPPD-QQRLIFAGKQLEDGRTLSDY 59 (76)
T ss_pred EEECCcCcHHHHHHHHHHHh--CCCHH-HeEEEECCEECCCCCcHHHc
Confidence 77889999999999999999 87754 56688999999999999763
No 22
>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=93.92 E-value=0.14 Score=35.63 Aligned_cols=58 Identities=22% Similarity=0.155 Sum_probs=44.6
Q ss_pred EEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHHHHHhccCCCCCeeEEE
Q psy7979 115 FIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFVYITRWRFRTPPLKLQY 179 (186)
Q Consensus 115 ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I~~~~W~~~~~Pm~L~Y 179 (186)
.+.++..+||+.||+-|+.+. +++.+. .-+.+.|.+|.++.||.+.-+ .. ..-+.|+|
T Consensus 15 ~~~v~~~~TV~~LK~~I~~~~--~~~~~~-qrLi~~Gk~L~D~~tL~~ygi---~~-~stv~l~~ 72 (73)
T cd01791 15 RVKCNPDDTIGDLKKLIAAQT--GTRPEK-IVLKKWYTIFKDHISLGDYEI---HD-GMNLELYY 72 (73)
T ss_pred EEEeCCCCcHHHHHHHHHHHh--CCChHH-EEEEeCCcCCCCCCCHHHcCC---CC-CCEEEEEe
Confidence 458899999999999999998 788664 446678999999999987421 12 34567766
No 23
>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=93.86 E-value=0.17 Score=34.77 Aligned_cols=46 Identities=22% Similarity=0.146 Sum_probs=39.9
Q ss_pred cEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHH
Q psy7979 114 RFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKF 162 (186)
Q Consensus 114 ~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~ 162 (186)
.-+.++...||..||.-|+.+. ++|.. +.-+.|+|.+|.++.||.+
T Consensus 11 ~~l~v~~~~tV~~lK~~i~~~~--gip~~-~q~Li~~Gk~L~D~~tL~~ 56 (74)
T cd01793 11 HTLEVTGQETVSDIKAHVAGLE--GIDVE-DQVLLLAGVPLEDDATLGQ 56 (74)
T ss_pred EEEEECCcCcHHHHHHHHHhhh--CCCHH-HEEEEECCeECCCCCCHHH
Confidence 3467888999999999999998 78765 5568899999999999987
No 24
>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=93.85 E-value=0.19 Score=33.63 Aligned_cols=46 Identities=17% Similarity=0.206 Sum_probs=39.1
Q ss_pred EEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHH
Q psy7979 115 FIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFV 163 (186)
Q Consensus 115 ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I 163 (186)
-+.+++..||..||+-|+.+. +++.. ..-++++|.+|.++.||.+.
T Consensus 14 ~~~v~~~~tv~~lK~~i~~~~--gi~~~-~q~L~~~g~~L~d~~~L~~~ 59 (72)
T cd01809 14 TFTVEEEITVLDLKEKIAEEV--GIPVE-QQRLIYSGRVLKDDETLSEY 59 (72)
T ss_pred EEEECCCCcHHHHHHHHHHHH--CcCHH-HeEEEECCEECCCcCcHHHC
Confidence 377788899999999999999 77644 56688899999999999874
No 25
>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=93.54 E-value=0.21 Score=33.96 Aligned_cols=45 Identities=18% Similarity=0.364 Sum_probs=38.6
Q ss_pred EEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHH
Q psy7979 116 IRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFV 163 (186)
Q Consensus 116 lrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I 163 (186)
+.++...||..||+-|+.+. +++. .+.-+.++|..|.++.||.+.
T Consensus 14 l~v~~~~TV~~lK~~I~~~~--~i~~-~~~~Li~~Gk~L~d~~tL~~~ 58 (71)
T cd01808 14 IEIAEDASVKDFKEAVSKKF--KANQ-EQLVLIFAGKILKDTDTLTQH 58 (71)
T ss_pred EEECCCChHHHHHHHHHHHh--CCCH-HHEEEEECCeEcCCCCcHHHc
Confidence 67788899999999999998 7664 466788899999999999774
No 26
>KOG0311|consensus
Probab=93.48 E-value=0.043 Score=49.19 Aligned_cols=42 Identities=24% Similarity=0.532 Sum_probs=35.3
Q ss_pred CcCCCCCCcccccccccCCccccccchhHHhhhHhhcccchhhHH
Q psy7979 8 KKIKNTCPSCNIIIHQSHPLQYISFDRTMQDLVYKLVPNLQANEM 52 (186)
Q Consensus 8 ~~~~~~CP~C~~~ih~s~Pl~~i~~D~tLQdIVyKLVPgL~~~E~ 52 (186)
+..++.||+|...+ -|+- .|+.|...-.|+++|+|+.-.-|+
T Consensus 76 r~gn~ecptcRk~l-~Skr--sLr~Dp~fdaLis~i~~sie~~e~ 117 (381)
T KOG0311|consen 76 RSGNNECPTCRKKL-VSKR--SLRIDPNFDALISKIYPSIEEYEA 117 (381)
T ss_pred HhcCCCCchHHhhc-cccc--cCCCCccHHHHHHHHhccHHHHhc
Confidence 56789999999999 4666 699999999999999999554443
No 27
>PTZ00044 ubiquitin; Provisional
Probab=93.45 E-value=0.22 Score=34.04 Aligned_cols=46 Identities=13% Similarity=0.140 Sum_probs=38.7
Q ss_pred EEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHH
Q psy7979 115 FIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFV 163 (186)
Q Consensus 115 ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I 163 (186)
-++++...||..||.-|+.+. ++|.. +.-+.|+|.+|.++.||.+-
T Consensus 14 ~l~v~~~~tv~~lK~~i~~~~--gi~~~-~q~L~~~g~~L~d~~~l~~~ 59 (76)
T PTZ00044 14 SFNFEPDNTVQQVKMALQEKE--GIDVK-QIRLIYSGKQMSDDLKLSDY 59 (76)
T ss_pred EEEECCCCcHHHHHHHHHHHH--CCCHH-HeEEEECCEEccCCCcHHHc
Confidence 367888999999999999999 88865 45577999999999998653
No 28
>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=93.32 E-value=0.19 Score=35.16 Aligned_cols=46 Identities=20% Similarity=0.262 Sum_probs=38.5
Q ss_pred cEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHH
Q psy7979 114 RFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFV 163 (186)
Q Consensus 114 ~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I 163 (186)
.-+..+..+||..||+-|+.+. +++.. +.-+.+.|.+|.++ ||.+.
T Consensus 14 ~~l~v~~~~TV~~LK~~I~~~~--~~~~~-~qrL~~~Gk~L~d~-~L~~~ 59 (78)
T cd01804 14 FDLSVPPDETVEGLKKRISQRL--KVPKE-RLALLHRETRLSSG-KLQDL 59 (78)
T ss_pred EEEEECCcCHHHHHHHHHHHHh--CCChH-HEEEEECCcCCCCC-cHHHc
Confidence 3477889999999999999998 77754 66788999999998 88763
No 29
>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=93.31 E-value=0.18 Score=33.81 Aligned_cols=45 Identities=24% Similarity=0.264 Sum_probs=38.3
Q ss_pred EEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHH
Q psy7979 116 IRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFV 163 (186)
Q Consensus 116 lrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I 163 (186)
+.++...||..||.-|+.+. +++.. +.-++++|..|.++.||.+.
T Consensus 14 i~v~~~~tv~~lK~~i~~~~--gi~~~-~q~L~~~g~~l~d~~~L~~~ 58 (71)
T cd01812 14 LSISSQATFGDLKKMLAPVT--GVEPR-DQKLIFKGKERDDAETLDMS 58 (71)
T ss_pred EEECCCCcHHHHHHHHHHhh--CCChH-HeEEeeCCcccCccCcHHHc
Confidence 67889999999999999998 88765 45578899999999888764
No 30
>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=93.00 E-value=0.37 Score=32.55 Aligned_cols=50 Identities=12% Similarity=0.092 Sum_probs=42.9
Q ss_pred ccEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHHH
Q psy7979 113 KRFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFVY 164 (186)
Q Consensus 113 ~~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I~ 164 (186)
.-.+++....|+.-|....+.+. +++....+.++++|+.|.++.|+.+.-
T Consensus 12 ~~~~~v~~~~~~~~l~~~~~~~~--~i~~~~~~~l~fdG~~L~~~~T~~~~~ 61 (72)
T PF11976_consen 12 EIKFKVKPTTTVSKLIEKYCEKK--GIPPEESIRLIFDGKRLDPNDTPEDLG 61 (72)
T ss_dssp EEEEEEETTSCCHHHHHHHHHHH--TTTT-TTEEEEETTEEE-TTSCHHHHT
T ss_pred EEEEEECCCCcHHHHHHHHHHhh--CCCccceEEEEECCEEcCCCCCHHHCC
Confidence 44678889999999999999999 888767999999999999999998763
No 31
>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=92.48 E-value=0.34 Score=35.98 Aligned_cols=47 Identities=15% Similarity=0.049 Sum_probs=40.2
Q ss_pred cEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHH
Q psy7979 114 RFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFV 163 (186)
Q Consensus 114 ~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I 163 (186)
--+.++...||..||..|+.+. +++.. +..+.|+|.+|.++.||.+.
T Consensus 40 ~~leV~~~~TV~~lK~kI~~~~--gip~~-~QrLi~~Gk~L~D~~tL~dy 86 (103)
T cd01802 40 FELRVSPFETVISVKAKIQRLE--GIPVA-QQHLIWNNMELEDEYCLNDY 86 (103)
T ss_pred EEEEeCCCCcHHHHHHHHHHHh--CCChH-HEEEEECCEECCCCCcHHHc
Confidence 3477889999999999999998 78755 56688999999999999774
No 32
>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=90.35 E-value=0.68 Score=32.98 Aligned_cols=61 Identities=15% Similarity=0.089 Sum_probs=42.9
Q ss_pred EEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHHHHHhccCCCCCeeEEE
Q psy7979 116 IRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFVYITRWRFRTPPLKLQY 179 (186)
Q Consensus 116 lrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I~~~~W~~~~~Pm~L~Y 179 (186)
+-|+...||.-||.-|+.... ..+...+.-+.|.|.+|.++.||.++-.. ....-.|+|-|
T Consensus 18 ve~~~~~TV~~lK~~i~~~~~-~~~~~~~QrLIy~GKiLkD~~tL~~~~~~--~~~~~tiHLV~ 78 (79)
T cd01790 18 VSCFLNWTVGELKTHLSRVYP-SKPLEQDQRLIYSGKLLPDHLKLRDVLRK--QDEYHMVHLVC 78 (79)
T ss_pred EecCCcChHHHHHHHHHHhcC-CCCChhHeEEEEcCeeccchhhHHHHhhc--ccCCceEEEEe
Confidence 445678899999999999873 23433455688889999999999987422 11134566654
No 33
>PF13881 Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB: 1SE9_A 1WGH_A 2GOW_A.
Probab=89.80 E-value=0.59 Score=35.27 Aligned_cols=54 Identities=13% Similarity=0.217 Sum_probs=39.6
Q ss_pred cEEEecccccHHHHHHHHHHHhhcCCC----CCceEEEEeCCEecCCCCcHHHHHHHh
Q psy7979 114 RFIRLSSQATITHLKKFVALKLLDEKS----KYKEIDILCNDELLGKDHTLKFVYITR 167 (186)
Q Consensus 114 ~ylrcs~~~tV~hLkKfL~~Kl~~~l~----~~~~veIlc~~~~L~~~~TL~~I~~~~ 167 (186)
.=+.+++..||..||.+|......+++ +...|-++|.|.+|.++-||.+.....
T Consensus 16 ~~~~~~~~~TV~~lKe~i~~~WP~d~~~~p~s~~~lRLI~~GriL~d~~tL~~~~~~~ 73 (111)
T PF13881_consen 16 GPFRFDPSTTVADLKERIWAEWPEDWEERPKSPSDLRLIYAGRILEDNKTLSDCRLPS 73 (111)
T ss_dssp EEEEE-TTSBHHHHHHHHHHSSSTTSSSTT-SGGGEEEEETTEEE-SSSBTGGGT--T
T ss_pred cccccCccChHHHHHHHHHHHCccccccCCCChhhEEEEeCCeecCCcCcHHHhCCCC
Confidence 345688899999999999987533433 246789999999999999998765333
No 34
>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=89.58 E-value=0.78 Score=32.14 Aligned_cols=43 Identities=14% Similarity=0.115 Sum_probs=37.1
Q ss_pred ecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHH
Q psy7979 118 LSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFV 163 (186)
Q Consensus 118 cs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I 163 (186)
.+...||+.||.-|..+. +++.. +.-+.|+|..|.++.||.+.
T Consensus 19 v~~~~TV~~lK~~i~~~~--gi~~~-~QrLi~~Gk~L~D~~tL~~y 61 (78)
T cd01797 19 LSRLTKVEELREKIQELF--NVEPE-CQRLFYRGKQMEDGHTLFDY 61 (78)
T ss_pred cCCcCcHHHHHHHHHHHh--CCCHH-HeEEEeCCEECCCCCCHHHc
Confidence 567899999999999998 78865 55688999999999999874
No 35
>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=88.90 E-value=4.1 Score=28.86 Aligned_cols=62 Identities=11% Similarity=0.208 Sum_probs=50.1
Q ss_pred CCceeEEEEeccCCCCccccccccEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHH
Q psy7979 91 DEQVNVYLECSVATTSSLKTLKKRFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFV 163 (186)
Q Consensus 91 de~vsl~LE~~~~~~~~l~~l~~~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I 163 (186)
.+.|.|.+... ....-++++....|+.-|+.-++.+. +++. .++-++++|..|.++.|+.+.
T Consensus 9 ~~~i~I~v~~~--------~g~~~~~~v~~~~~l~~l~~~y~~~~--gi~~-~~~rf~f~G~~L~~~~T~~~l 70 (87)
T cd01763 9 SEHINLKVKGQ--------DGNEVFFKIKRSTPLKKLMEAYCQRQ--GLSM-NSVRFLFDGQRIRDNQTPDDL 70 (87)
T ss_pred CCeEEEEEECC--------CCCEEEEEEcCCCHHHHHHHHHHHHh--CCCc-cceEEEECCeECCCCCCHHHc
Confidence 34577777322 23455789999999999999999999 8875 588899999999999999875
No 36
>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=88.54 E-value=0.8 Score=31.92 Aligned_cols=46 Identities=22% Similarity=0.317 Sum_probs=37.4
Q ss_pred EEEecccccHHHHHHHHHHHhhcCCCCCceEEE--EeCCEecCCCCcHHHH
Q psy7979 115 FIRLSSQATITHLKKFVALKLLDEKSKYKEIDI--LCNDELLGKDHTLKFV 163 (186)
Q Consensus 115 ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veI--lc~~~~L~~~~TL~~I 163 (186)
.+.++...||..||+-|+.+. +++.. +.-+ .++|.+|.++.||.+.
T Consensus 16 ~~~v~~~~TV~~lK~~I~~~~--~i~~~-~qrL~~~~~G~~L~D~~tL~~~ 63 (80)
T cd01792 16 LVSLRDSMTVSELKQQIAQKI--GVPAF-QQRLAHLDSREVLQDGVPLVSQ 63 (80)
T ss_pred EEEcCCCCcHHHHHHHHHHHh--CCCHH-HEEEEeccCCCCCCCCCCHHHc
Confidence 356778899999999999998 77754 4445 6789999999999764
No 37
>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=88.47 E-value=1.4 Score=30.39 Aligned_cols=46 Identities=11% Similarity=0.113 Sum_probs=37.9
Q ss_pred EEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHHH
Q psy7979 116 IRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFVY 164 (186)
Q Consensus 116 lrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I~ 164 (186)
+..+...||..||.-|..+. ++|... .-++++|..|.++.||.+.-
T Consensus 12 l~v~~~~TV~~lK~~i~~~~--gip~~~-q~L~~~G~~L~d~~tL~~~~ 57 (76)
T cd01800 12 FTLQLSDPVSVLKVKIHEET--GMPAGK-QKLQYEGIFIKDSNSLAYYN 57 (76)
T ss_pred EEECCCCcHHHHHHHHHHHH--CCCHHH-EEEEECCEEcCCCCcHHHcC
Confidence 45567889999999999998 888664 45778999999999997653
No 38
>KOG0308|consensus
Probab=88.02 E-value=0.29 Score=47.11 Aligned_cols=41 Identities=34% Similarity=0.685 Sum_probs=36.3
Q ss_pred ceEEEEeC--------C------EecCCCCcHHHHHHHhccCCCCCeeEEEeeccc
Q psy7979 143 KEIDILCN--------D------ELLGKDHTLKFVYITRWRFRTPPLKLQYRPRID 184 (186)
Q Consensus 143 ~~veIlc~--------~------~~L~~~~TL~~I~~~~W~~~~~Pm~L~Yr~~~~ 184 (186)
..||++|| | ++|.+++||.-|.-+.||. .+-+.|+||..+.
T Consensus 667 e~iellcn~~~f~~~~D~~~~~fqVldPdM~L~TVr~~iWKs-~gDlvl~Yr~k~~ 721 (735)
T KOG0308|consen 667 EKIELLCNKALFRDPTDLPRISFQVLDPDMDLRTVRHLIWKS-SGDLVLHYRVKVH 721 (735)
T ss_pred hhhHHHhccccccCcCCccccceEEeCCCCcHHHhhhheecC-CCcEEEEEeeecc
Confidence 35789999 8 9999999999999999995 7899999998753
No 39
>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=86.28 E-value=2.3 Score=25.42 Aligned_cols=45 Identities=27% Similarity=0.280 Sum_probs=36.2
Q ss_pred ccEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcH
Q psy7979 113 KRFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTL 160 (186)
Q Consensus 113 ~~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL 160 (186)
..-+.++...||..|++.|+.++ +.+ ...+.++++|..+.+..++
T Consensus 9 ~~~~~~~~~~tv~~l~~~i~~~~--~~~-~~~~~l~~~~~~~~~~~~~ 53 (69)
T cd00196 9 TVELLVPSGTTVADLKEKLAKKL--GLP-PEQQRLLVNGKILPDSLTL 53 (69)
T ss_pred EEEEEcCCCCcHHHHHHHHHHHH--CcC-hHHeEEEECCeECCCCCcH
Confidence 33466778999999999999999 543 4577889999888888776
No 40
>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=85.25 E-value=1.9 Score=32.38 Aligned_cols=44 Identities=16% Similarity=0.229 Sum_probs=31.1
Q ss_pred EEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecC-CCCcHH
Q psy7979 115 FIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLG-KDHTLK 161 (186)
Q Consensus 115 ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~-~~~TL~ 161 (186)
=|-|++.+||..||..|++++ +++.+.+= ++++|..|. +.-||.
T Consensus 18 ~L~V~~~~TVg~LK~lImQ~f--~V~P~dQk-L~~dG~~L~DDsrTLs 62 (107)
T cd01795 18 ALLVSANQTLKELKIQIMHAF--SVAPFDQN-LSIDGKILSDDCATLG 62 (107)
T ss_pred eEEeCccccHHHHHHHHHHHh--cCCcccce-eeecCceeccCCccHH
Confidence 456899999999999999999 88877554 333454433 334443
No 41
>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=84.73 E-value=4.4 Score=28.16 Aligned_cols=45 Identities=18% Similarity=0.134 Sum_probs=35.8
Q ss_pred EEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecC-CCCcHHHH
Q psy7979 115 FIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLG-KDHTLKFV 163 (186)
Q Consensus 115 ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~-~~~TL~~I 163 (186)
-+.++...||..||.-|..+. ++|...+. + ++|..|. ++.||.+.
T Consensus 16 ~l~v~~~~TV~~lK~kI~~~~--gip~~~Qr-L-~~G~~L~dD~~tL~~y 61 (75)
T cd01799 16 WLTVRPDMTVAQLKDKVFLDY--GFPPAVQR-W-VIGQRLARDQETLYSH 61 (75)
T ss_pred EEEECCCCcHHHHHHHHHHHH--CcCHHHEE-E-EcCCeeCCCcCCHHHc
Confidence 477788999999999999999 88866543 5 7887774 66898764
No 42
>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=83.78 E-value=2.4 Score=29.36 Aligned_cols=46 Identities=15% Similarity=0.162 Sum_probs=38.3
Q ss_pred EEecccccHHHHHHHHHHHhhcCCCCCceEEEEe---CCEecCCCCcHHHHH
Q psy7979 116 IRLSSQATITHLKKFVALKLLDEKSKYKEIDILC---NDELLGKDHTLKFVY 164 (186)
Q Consensus 116 lrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc---~~~~L~~~~TL~~I~ 164 (186)
+.++...||..||.-|..+. ++|...+= +++ .|.++.++.||...-
T Consensus 14 v~v~~~~Tv~~lK~~i~~~t--gvp~~~QK-Li~~~~~Gk~l~D~~~L~~~~ 62 (74)
T cd01813 14 VTTLSEDTVLDLKQFIKTLT--GVLPERQK-LLGLKVKGKPAEDDVKISALK 62 (74)
T ss_pred EEECCCCCHHHHHHHHHHHH--CCCHHHEE-EEeecccCCcCCCCcCHHHcC
Confidence 78889999999999999999 78866443 554 788999999998763
No 43
>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=82.43 E-value=2.2 Score=31.44 Aligned_cols=45 Identities=16% Similarity=0.288 Sum_probs=37.4
Q ss_pred ecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHH
Q psy7979 118 LSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFV 163 (186)
Q Consensus 118 cs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I 163 (186)
-++.+||..||+.|+.++. .-.+...+-+.|+|..|.++-.|.-+
T Consensus 20 ~~~~~Tv~~LK~lIR~~~p-~~~s~~rLRlI~~Gr~L~d~t~l~~~ 64 (97)
T PF10302_consen 20 SPNTTTVAWLKQLIRERLP-PEPSRRRLRLIYAGRLLNDHTDLSSE 64 (97)
T ss_pred CCCcccHHHHHHHHHhhcC-CCCccccEEeeecCcccCccchhhhh
Confidence 3588999999999999984 23456789999999999999999753
No 44
>KOG3439|consensus
Probab=80.49 E-value=23 Score=27.00 Aligned_cols=83 Identities=17% Similarity=0.187 Sum_probs=63.7
Q ss_pred ceeEEEEeccCCCCccccccccEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCE-ecCCCCcHHHHHHHhccCC
Q psy7979 93 QVNVYLECSVATTSSLKTLKKRFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDE-LLGKDHTLKFVYITRWRFR 171 (186)
Q Consensus 93 ~vsl~LE~~~~~~~~l~~l~~~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~-~L~~~~TL~~I~~~~W~~~ 171 (186)
.|.|.|... .+.+.++++=..+++.-|+.-+-.||.+.| .|+...++=++.|+- .=.++.+...+|+-.- -
T Consensus 30 kV~i~l~ai----G~~PilK~~k~~i~~t~tfa~vi~Flkk~L--kl~as~slflYVN~sFAPsPDq~v~~Ly~cf~--~ 101 (116)
T KOG3439|consen 30 KVQIRLRAI----GDAPILKKSKFKINPTQTFAKVILFLKKFL--KLQASDSLFLYVNNSFAPSPDQIVGNLYECFG--T 101 (116)
T ss_pred eEEEEEecc----CCCcceecceEEeCcchhhHHHHHHHHHHh--CCcccCeEEEEEcCccCCCchhHHHHHHHhcC--C
Confidence 366766554 246678888899999999999999999999 899888987888763 3445677777775443 3
Q ss_pred CCCeeEEEeecc
Q psy7979 172 TPPLKLQYRPRI 183 (186)
Q Consensus 172 ~~Pm~L~Yr~~~ 183 (186)
+.-|+|.|-++.
T Consensus 102 d~~Lvl~Yc~s~ 113 (116)
T KOG3439|consen 102 DGKLVLNYCISV 113 (116)
T ss_pred CCEEEEEEeeec
Confidence 679999998764
No 45
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=76.59 E-value=1.5 Score=27.20 Aligned_cols=25 Identities=36% Similarity=0.756 Sum_probs=19.6
Q ss_pred CCccccCcCCCCCCcccccccccCC
Q psy7979 2 LDKGDKKKIKNTCPSCNIIIHQSHP 26 (186)
Q Consensus 2 ~~~~~~~~~~~~CP~C~~~ih~s~P 26 (186)
||-|-+.-....||+|++.-....|
T Consensus 4 Ld~gq~~~~~~~C~~CgM~Y~~~~~ 28 (41)
T PF13878_consen 4 LDLGQKSFGATTCPTCGMLYSPGSP 28 (41)
T ss_pred EeCCCCccCCcCCCCCCCEECCCCH
Confidence 6778777778999999999755444
No 46
>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=76.06 E-value=5.6 Score=36.15 Aligned_cols=46 Identities=15% Similarity=0.258 Sum_probs=38.4
Q ss_pred EEEecccccHHHHHHHHHHHhhcC---CCCCceEEEEeCCEecCCCCcHHHH
Q psy7979 115 FIRLSSQATITHLKKFVALKLLDE---KSKYKEIDILCNDELLGKDHTLKFV 163 (186)
Q Consensus 115 ylrcs~~~tV~hLkKfL~~Kl~~~---l~~~~~veIlc~~~~L~~~~TL~~I 163 (186)
-|.++...||..||+.|..+. + ++. .+.-++|+|.+|.++.||.+.
T Consensus 14 ~IeV~~~~TV~dLK~kI~~~~--g~~~ip~-~~QkLIy~GkiL~Dd~tL~dy 62 (378)
T TIGR00601 14 KIDMEPDETVKELKEKIEAEQ--GKDAYPV-AQQKLIYSGKILSDDKTVREY 62 (378)
T ss_pred EEEeCCcChHHHHHHHHHHhh--CCCCCCh-hHeEEEECCEECCCCCcHHHc
Confidence 467788999999999999987 5 554 356688999999999999874
No 47
>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=67.94 E-value=9.6 Score=29.03 Aligned_cols=48 Identities=17% Similarity=0.239 Sum_probs=36.2
Q ss_pred EecccccHHHHHHHHHHHhhc---CCC-CCceEEEEeCCEecCCCCcHHHHH
Q psy7979 117 RLSSQATITHLKKFVALKLLD---EKS-KYKEIDILCNDELLGKDHTLKFVY 164 (186)
Q Consensus 117 rcs~~~tV~hLkKfL~~Kl~~---~l~-~~~~veIlc~~~~L~~~~TL~~I~ 164 (186)
+++...||..||.-|...-.. .+| ...++-+.|.|.+|.++.||.+..
T Consensus 21 ~~~~sdTV~~lKekI~~~~p~~ke~~P~~~~~qKLIysGKiLeD~~TL~d~~ 72 (113)
T cd01814 21 RYPAATTVDFLKERVVSQWPKDKEVGPKTVNEVKLISAGKILENSKTVGECR 72 (113)
T ss_pred ccChhhHHHHHHHHHHHhcccccccCCCCHHHeEEEeCCeecCCCCcHHHhC
Confidence 567999999999999865411 122 134677889999999999998753
No 48
>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=67.59 E-value=11 Score=28.90 Aligned_cols=65 Identities=22% Similarity=0.252 Sum_probs=48.8
Q ss_pred ccEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHH--HHHhccCC-CCCeeEEEe
Q psy7979 113 KRFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFV--YITRWRFR-TPPLKLQYR 180 (186)
Q Consensus 113 ~~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I--~~~~W~~~-~~Pm~L~Yr 180 (186)
.-|+.|-...||..|||-|..-+ +.|.+.+- ++-.+++|.++-||.+- --+.-|.+ .+.+-|.||
T Consensus 13 TiF~dakes~tVlelK~~iegI~--k~pp~dQr-L~kd~qvLeD~kTL~d~g~t~~~akaq~pA~vgLa~r 80 (119)
T cd01788 13 TIFTDAKESTTVYELKRIVEGIL--KRPPEDQR-LYKDDQLLDDGKTLGDCGFTSQTARPQAPATVGLAFR 80 (119)
T ss_pred EEEeecCCcccHHHHHHHHHHHh--cCChhHhe-eecCceeecccccHHHcCccccccccCCCCeEEEEEe
Confidence 34899999999999999999999 88877665 33557899999999874 22333332 345777777
No 49
>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis. PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain
Probab=67.00 E-value=22 Score=25.44 Aligned_cols=60 Identities=20% Similarity=0.216 Sum_probs=42.4
Q ss_pred EEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecC-----CCCcHHHHHHHhccCCCCCeeEEEe
Q psy7979 115 FIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLG-----KDHTLKFVYITRWRFRTPPLKLQYR 180 (186)
Q Consensus 115 ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~-----~~~TL~~I~~~~W~~~~~Pm~L~Yr 180 (186)
=||+|..++...|..-|+.|| +++ ..++-+.|.++.=+ .+-.|++++-. .+++-+.|+..
T Consensus 14 aIrvp~~~~y~~L~~ki~~kL--kl~-~e~i~LsYkde~s~~~v~l~d~dle~aws~---~~~~~lTLwC~ 78 (80)
T cd06406 14 AIQVARGLSYATLLQKISSKL--ELP-AEHITLSYKSEASGEDVILSDTNMEDVWSQ---AKDGCLTLWCT 78 (80)
T ss_pred EEEcCCCCCHHHHHHHHHHHh--CCC-chhcEEEeccCCCCCccCcChHHHHHHHHh---hcCCeEEEEEe
Confidence 478899999999999999999 998 45688888754322 45555555421 23567777654
No 50
>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=63.08 E-value=45 Score=22.62 Aligned_cols=62 Identities=16% Similarity=0.171 Sum_probs=47.2
Q ss_pred EEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCC-----EecCCCCcHHHHHHHhccCCCCCeeEEE
Q psy7979 115 FIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCND-----ELLGKDHTLKFVYITRWRFRTPPLKLQY 179 (186)
Q Consensus 115 ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~-----~~L~~~~TL~~I~~~~W~~~~~Pm~L~Y 179 (186)
.+..+..++...|..-|+.++ +++ ...+.|.|.+ .++..+--|..+..........+|+|+=
T Consensus 15 ~~~~~~~~s~~~L~~~i~~~~--~~~-~~~~~l~Y~D~dgD~V~i~sd~Dl~~a~~~~~~~~~~~lrl~v 81 (84)
T PF00564_consen 15 IISLPSDVSFDDLRSKIREKF--GLL-DEDFQLKYKDEDGDLVTISSDEDLQEAIEQAKESGSKTLRLFV 81 (84)
T ss_dssp EEEECSTSHHHHHHHHHHHHH--TTS-TSSEEEEEEETTSSEEEESSHHHHHHHHHHHHHCTTSCEEEEE
T ss_pred EEEcCCCCCHHHHHHHHHHHh--CCC-CccEEEEeeCCCCCEEEeCCHHHHHHHHHHHHhcCCCcEEEEE
Confidence 578888899999999999999 655 5678888853 5777777787776666653345888864
No 51
>cd01775 CYR1_RA Ubiquitin domain of CYR1 adenylate cyclase. CYR1 is a fungal adenylate cyclase with at least four domains, an N-terminal RA (Ras association) domain, a middle leucine-rich repeat domain, a catalytic domain. The N-terminal RA domain of CYR1 post-translationally modifies a small GTPase called Ras. The Ras-CYR1 pathway has been implicated in the transduction of a glucose-triggered signal to an intracellular environment where a protein phosphorylation cascade is initiated by cyclic AMP.
Probab=60.93 E-value=28 Score=25.81 Aligned_cols=38 Identities=13% Similarity=0.107 Sum_probs=29.8
Q ss_pred cEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCC
Q psy7979 114 RFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCND 151 (186)
Q Consensus 114 ~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~ 151 (186)
.-+.||-++||..|-+-|.+|+++.-+.++++-+-++|
T Consensus 15 ~Tls~~l~tTv~eli~~L~rK~~l~~~~ny~l~l~~~~ 52 (97)
T cd01775 15 TTLSCPLNTTVSELIPQLAKKFYLPSGGNYQLSLKKHD 52 (97)
T ss_pred EEEEcCCcCcHHHHHHHHHHhhcCCCCCCeEEEEEECC
Confidence 46889999999999999999995444455677666665
No 52
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=60.92 E-value=4.2 Score=22.88 Aligned_cols=11 Identities=36% Similarity=0.999 Sum_probs=9.0
Q ss_pred CCCCccccccc
Q psy7979 12 NTCPSCNIIIH 22 (186)
Q Consensus 12 ~~CP~C~~~ih 22 (186)
+.||.|+..|-
T Consensus 1 K~CP~C~~~V~ 11 (26)
T PF10571_consen 1 KTCPECGAEVP 11 (26)
T ss_pred CcCCCCcCCch
Confidence 57999999883
No 53
>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=60.75 E-value=21 Score=24.49 Aligned_cols=43 Identities=28% Similarity=0.257 Sum_probs=31.7
Q ss_pred cccccHHHHHHHHHHHhhcCCCCCceEEEE--eCCEecCCCCcHHHH
Q psy7979 119 SSQATITHLKKFVALKLLDEKSKYKEIDIL--CNDELLGKDHTLKFV 163 (186)
Q Consensus 119 s~~~tV~hLkKfL~~Kl~~~l~~~~~veIl--c~~~~L~~~~TL~~I 163 (186)
|..+||..||+-|+.+. .....+++-+. ..|.+|.++-||.+.
T Consensus 20 ~~~aTV~dlk~~i~~~~--~~~~~~Rqrl~~~~~g~~L~d~~tL~~~ 64 (77)
T cd01801 20 SGDATIADLKKLIAKSS--PQLTVNRQSLRLEPKGKSLKDDDTLVDL 64 (77)
T ss_pred CCCccHHHHHHHHHHHc--CCCCcceeEEEeCCCCcccCCcccHhhc
Confidence 67899999999999886 44333454443 468899888888653
No 54
>KOG0010|consensus
Probab=60.70 E-value=10 Score=35.58 Aligned_cols=47 Identities=21% Similarity=0.374 Sum_probs=39.2
Q ss_pred ccEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHH
Q psy7979 113 KRFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKF 162 (186)
Q Consensus 113 ~~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~ 162 (186)
+.=+.++...||..||--|+.++ +.+.+ ++.+.|.|.+|.++.||.+
T Consensus 26 k~~~~V~~~ssV~qlKE~I~~~f--~a~~d-qlvLIfaGrILKD~dTL~~ 72 (493)
T KOG0010|consen 26 KYEVNVASDSSVLQLKELIAQRF--GAPPD-QLVLIYAGRILKDDDTLKQ 72 (493)
T ss_pred ceeEecccchHHHHHHHHHHHhc--CCChh-HeeeeecCccccChhhHHH
Confidence 55677889999999999999999 87755 5556666899999999975
No 55
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=60.68 E-value=3.5 Score=23.54 Aligned_cols=11 Identities=36% Similarity=0.936 Sum_probs=6.4
Q ss_pred CCCcccccccc
Q psy7979 13 TCPSCNIIIHQ 23 (186)
Q Consensus 13 ~CP~C~~~ih~ 23 (186)
+||+|+..+++
T Consensus 1 ~CP~C~s~l~~ 11 (28)
T PF03119_consen 1 TCPVCGSKLVR 11 (28)
T ss_dssp B-TTT--BEEE
T ss_pred CcCCCCCEeEc
Confidence 59999999864
No 56
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=55.89 E-value=5.3 Score=21.71 Aligned_cols=13 Identities=23% Similarity=0.636 Sum_probs=8.1
Q ss_pred CcCCCCCCccccc
Q psy7979 8 KKIKNTCPSCNII 20 (186)
Q Consensus 8 ~~~~~~CP~C~~~ 20 (186)
..++++||.|+..
T Consensus 10 ~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 10 EDDAKFCPNCGTP 22 (23)
T ss_pred CCcCcchhhhCCc
Confidence 3455777777654
No 57
>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=55.84 E-value=31 Score=24.25 Aligned_cols=35 Identities=23% Similarity=0.157 Sum_probs=26.1
Q ss_pred EEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCE
Q psy7979 116 IRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDE 152 (186)
Q Consensus 116 lrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~ 152 (186)
.|.|..+||..||.=|.... +++...+--+++.+.
T Consensus 17 kr~~~~~Tv~~lK~kl~~~~--G~~~~~mrL~l~~~~ 51 (84)
T cd01789 17 KKYSRGLTIAELKKKLELVV--GTPASSMRLQLFDGD 51 (84)
T ss_pred EecCCCCcHHHHHHHHHHHH--CCCccceEEEEEcCC
Confidence 46799999999999999998 777654433345543
No 58
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=52.87 E-value=6.3 Score=21.84 Aligned_cols=10 Identities=30% Similarity=0.850 Sum_probs=5.1
Q ss_pred CCCCCCcccc
Q psy7979 10 IKNTCPSCNI 19 (186)
Q Consensus 10 ~~~~CP~C~~ 19 (186)
+.++||.|+.
T Consensus 15 ~~~fC~~CG~ 24 (26)
T PF13248_consen 15 DAKFCPNCGA 24 (26)
T ss_pred ccccChhhCC
Confidence 3455555554
No 59
>PF14353 CpXC: CpXC protein
Probab=51.97 E-value=7.3 Score=29.39 Aligned_cols=48 Identities=21% Similarity=0.433 Sum_probs=35.3
Q ss_pred CCCCCcccccccccCCccccccchhHHhhhHhhcccchhhHHHHHHHHHHHhC
Q psy7979 11 KNTCPSCNIIIHQSHPLQYISFDRTMQDLVYKLVPNLQANEMKREREFYRIRG 63 (186)
Q Consensus 11 ~~~CP~C~~~ih~s~Pl~~i~~D~tLQdIVyKLVPgL~~~E~~rr~eFy~~~~ 63 (186)
..+||.|+....-..|+.|.-+++ ..+.-++|. ..+.+...+|+....
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~D~~~---~~~i~~~P~--~~~~~~~~~~~~~~~ 85 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYHDPEK---KFMIYYFPD--NQDEEEQEQFLGDLS 85 (128)
T ss_pred EEECCCCCCceecCCCEEEEcCCC---CEEEEEcCC--cchHHHHHHHHHhhc
Confidence 478999999999899987776664 455567888 455666667776543
No 60
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=50.84 E-value=7.5 Score=22.82 Aligned_cols=20 Identities=20% Similarity=0.576 Sum_probs=16.7
Q ss_pred ccccCcCCCCCCcccccccc
Q psy7979 4 KGDKKKIKNTCPSCNIIIHQ 23 (186)
Q Consensus 4 ~~~~~~~~~~CP~C~~~ih~ 23 (186)
+++.+++...|..|++.++.
T Consensus 9 ~k~rk~T~~~C~~C~v~lC~ 28 (32)
T PF13842_consen 9 KKRRKDTRYMCSKCDVPLCV 28 (32)
T ss_pred CCccceeEEEccCCCCcccC
Confidence 56777799999999988874
No 61
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=49.09 E-value=7.5 Score=25.45 Aligned_cols=17 Identities=29% Similarity=0.669 Sum_probs=13.1
Q ss_pred CccccCcCCCCCCcccc
Q psy7979 3 DKGDKKKIKNTCPSCNI 19 (186)
Q Consensus 3 ~~~~~~~~~~~CP~C~~ 19 (186)
|.+.++-.+..||.|+-
T Consensus 11 ~~~kv~rk~~~CPrCG~ 27 (51)
T COG1998 11 DDEKVKRKNRFCPRCGP 27 (51)
T ss_pred cCCcEEEccccCCCCCC
Confidence 33447888999999993
No 62
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=47.21 E-value=14 Score=25.46 Aligned_cols=25 Identities=20% Similarity=0.594 Sum_probs=11.5
Q ss_pred CCCCcccccccccCCccccccchhHHhhh
Q psy7979 12 NTCPSCNIIIHQSHPLQYISFDRTMQDLV 40 (186)
Q Consensus 12 ~~CP~C~~~ih~s~Pl~~i~~D~tLQdIV 40 (186)
..||+|++..+.. -++--|+|+++|
T Consensus 41 ~~CPvC~~Paw~q----D~~~NrqLd~~i 65 (65)
T PF14835_consen 41 SECPVCHTPAWIQ----DIQINRQLDSMI 65 (65)
T ss_dssp TB-SSS--B-S-S----S----HHHHHHH
T ss_pred CCCCCcCChHHHH----HHHhhhhhhccC
Confidence 4699999988642 356777888775
No 63
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=46.70 E-value=11 Score=25.14 Aligned_cols=24 Identities=29% Similarity=0.548 Sum_probs=18.0
Q ss_pred CCCCCcccccccccCCccccccchh
Q psy7979 11 KNTCPSCNIIIHQSHPLQYISFDRT 35 (186)
Q Consensus 11 ~~~CP~C~~~ih~s~Pl~~i~~D~t 35 (186)
+..||.|+.....++|- -..+|..
T Consensus 17 k~~CP~CG~~t~~~~P~-rfSp~D~ 40 (56)
T PRK13130 17 KEICPVCGGKTKNPHPP-RFSPEDK 40 (56)
T ss_pred cccCcCCCCCCCCCCCC-CCCCCCc
Confidence 67899999999888885 4445543
No 64
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=46.32 E-value=7.7 Score=23.21 Aligned_cols=15 Identities=27% Similarity=0.724 Sum_probs=6.1
Q ss_pred CCCCcccccccccCC
Q psy7979 12 NTCPSCNIIIHQSHP 26 (186)
Q Consensus 12 ~~CP~C~~~ih~s~P 26 (186)
++||.|+..+...-|
T Consensus 1 kfC~~CG~~l~~~ip 15 (34)
T PF14803_consen 1 KFCPQCGGPLERRIP 15 (34)
T ss_dssp -B-TTT--B-EEE--
T ss_pred CccccccChhhhhcC
Confidence 589999988854444
No 65
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=46.28 E-value=11 Score=25.39 Aligned_cols=13 Identities=31% Similarity=0.744 Sum_probs=10.7
Q ss_pred cCCCCCCcccccc
Q psy7979 9 KIKNTCPSCNIII 21 (186)
Q Consensus 9 ~~~~~CP~C~~~i 21 (186)
|..++||.|+..|
T Consensus 1 e~HkHC~~CG~~I 13 (59)
T PF09889_consen 1 EPHKHCPVCGKPI 13 (59)
T ss_pred CCCCcCCcCCCcC
Confidence 3468999999888
No 66
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=45.81 E-value=9.5 Score=21.28 Aligned_cols=9 Identities=33% Similarity=0.907 Sum_probs=8.0
Q ss_pred CCCcccccc
Q psy7979 13 TCPSCNIII 21 (186)
Q Consensus 13 ~CP~C~~~i 21 (186)
.||+|+..+
T Consensus 3 ~CPiC~~~v 11 (26)
T smart00734 3 QCPVCFREV 11 (26)
T ss_pred cCCCCcCcc
Confidence 699999887
No 67
>cd06411 PB1_p51 The PB1 domain is present in the p51 protein, a homolog of the p67 protein. p51 plays an important role in NADPH oxidase activation during phagosytosis. The PB1 domain is a modular domain mediating specific protein-protein interaction in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain mo
Probab=45.32 E-value=1.1e+02 Score=21.76 Aligned_cols=59 Identities=15% Similarity=0.252 Sum_probs=43.8
Q ss_pred EEecccccHHHHHHHHHHHhhcCCCCCceEEEEeC----C---EecCCCCcHHHHHHHhccCCCCCeeEEEe
Q psy7979 116 IRLSSQATITHLKKFVALKLLDEKSKYKEIDILCN----D---ELLGKDHTLKFVYITRWRFRTPPLKLQYR 180 (186)
Q Consensus 116 lrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~----~---~~L~~~~TL~~I~~~~W~~~~~Pm~L~Yr 180 (186)
|++|..++...|.-.|+.|| .++..+ +-+-|. + +++..+-+|+++|..- +++|+.|+..
T Consensus 11 i~v~~g~~y~~L~~~ls~kL--~l~~~~-~~LSY~~~~~~~~~v~l~~e~~me~aW~~v---~~~~ltLwcq 76 (78)
T cd06411 11 LRAPRGADVSSLRALLSQAL--PQQAQR-GQLSYRAPGEDGHWVPISGEESLQRAWQDV---ADGPRGLQLQ 76 (78)
T ss_pred EEccCCCCHHHHHHHHHHHh--cCChhh-cEEEecCCCCCccEeecCcchHHHHHHHhc---cCCceEEEEe
Confidence 67889999999999999999 777653 555553 1 3677788898886332 3678887754
No 68
>PF05080 DUF681: Protein of unknown function (DUF681); InterPro: IPR007772 This entry is represented by Beak and feather disease virus (BFDV), Orf5; it is a family of uncharacterised viral proteins.
Probab=44.12 E-value=3.3 Score=29.98 Aligned_cols=25 Identities=32% Similarity=0.317 Sum_probs=20.6
Q ss_pred EEEecccccHHHHHHHHHHHhhcCCC
Q psy7979 115 FIRLSSQATITHLKKFVALKLLDEKS 140 (186)
Q Consensus 115 ylrcs~~~tV~hLkKfL~~Kl~~~l~ 140 (186)
.-||||.+||.|+|=-|+.-|| .|+
T Consensus 74 iarcsasatvthikcqlra~lw-sl~ 98 (101)
T PF05080_consen 74 IARCSASATVTHIKCQLRALLW-SLP 98 (101)
T ss_pred EEEeeeeeEEEEEeeeehhhhc-cCc
Confidence 4589999999999988887776 554
No 69
>KOG3493|consensus
Probab=43.75 E-value=3.9 Score=28.35 Aligned_cols=49 Identities=22% Similarity=0.193 Sum_probs=30.5
Q ss_pred cccEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHH
Q psy7979 112 KKRFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFV 163 (186)
Q Consensus 112 ~~~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I 163 (186)
++-=++|-+.-||+.+||.||..-+ ..+ ..+-+---..++.++-||++.
T Consensus 12 KKVRvKCn~dDtiGD~KKliaaQtG-T~~--~kivl~k~~~i~kd~I~L~dy 60 (73)
T KOG3493|consen 12 KKVRVKCNTDDTIGDLKKLIAAQTG-TRP--EKIVLKKWYTIFKDHITLSDY 60 (73)
T ss_pred ceEEEEeCCcccccCHHHHHHHhhC-CCh--hHhHHHhhhhhhhcccceeeE
Confidence 3445889999999999999999984 212 222221112355556666543
No 70
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=43.49 E-value=40 Score=23.07 Aligned_cols=46 Identities=22% Similarity=0.293 Sum_probs=31.3
Q ss_pred EEEeccc-ccHHHHHHHHHHHhhcCCC-CCceEEEEeCCEecCCCCcHH
Q psy7979 115 FIRLSSQ-ATITHLKKFVALKLLDEKS-KYKEIDILCNDELLGKDHTLK 161 (186)
Q Consensus 115 ylrcs~~-~tV~hLkKfL~~Kl~~~l~-~~~~veIlc~~~~L~~~~TL~ 161 (186)
-+.++.. .||..|...|..++. ++- ....+-|++|++....+..|+
T Consensus 19 ~~~~~~~~~tv~~L~~~L~~~~p-~l~~~~~~~~v~vn~~~v~~~~~l~ 66 (80)
T TIGR01682 19 TLELPDESTTVGELKEHLAKEGP-ELAASRGQVMVAVNEEYVTDDALLN 66 (80)
T ss_pred EEECCCCCcCHHHHHHHHHHhCc-hhhhhccceEEEECCEEcCCCcCcC
Confidence 3455555 899999999999983 221 123466888998887655543
No 71
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=42.13 E-value=42 Score=23.77 Aligned_cols=62 Identities=23% Similarity=0.231 Sum_probs=40.6
Q ss_pred cEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCE-----ecCCCCcHHH-HHHHhccCCCCCeeEE
Q psy7979 114 RFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDE-----LLGKDHTLKF-VYITRWRFRTPPLKLQ 178 (186)
Q Consensus 114 ~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~-----~L~~~~TL~~-I~~~~W~~~~~Pm~L~ 178 (186)
.=++.|..++...|+.=|+.++ ++.....+.|-|.++ .|..+.=|+. +.+++--+ ..-++|+
T Consensus 12 ~r~~l~~~~~~~~L~~~i~~r~--~~~~~~~f~LkY~Ddegd~v~ltsd~DL~eai~i~~~~~-~~~v~l~ 79 (82)
T cd06407 12 IRFRLPPSWGFTELKQEIAKRF--KLDDMSAFDLKYLDDDEEWVLLTCDADLEECIDVYRSSG-SHTIRLL 79 (82)
T ss_pred EEEEcCCCCCHHHHHHHHHHHh--CCCCCCeeEEEEECCCCCeEEeecHHHHHHHHHHHHHCC-CCeEEEE
Confidence 3467788999999999999999 776557888888754 4444444544 23333322 3445554
No 72
>KOG0006|consensus
Probab=41.35 E-value=32 Score=31.05 Aligned_cols=40 Identities=23% Similarity=0.359 Sum_probs=33.8
Q ss_pred cccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHH
Q psy7979 119 SSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLK 161 (186)
Q Consensus 119 s~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~ 161 (186)
.....|..||+.++.++ ++++ .+++|...|..|.++.|++
T Consensus 21 ~~~t~I~~lke~Vak~~--gvp~-D~L~viFaGKeLs~~ttv~ 60 (446)
T KOG0006|consen 21 DSDTSIFQLKEVVAKRQ--GVPA-DQLRVIFAGKELSNDTTVQ 60 (446)
T ss_pred ecCCCHHHHHHHHHHhh--CCCh-hheEEEEeccccccCceee
Confidence 45568999999999999 8885 4788777788999999987
No 73
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=38.87 E-value=13 Score=24.05 Aligned_cols=17 Identities=35% Similarity=0.808 Sum_probs=12.1
Q ss_pred CccccCcCCCCCCcccc
Q psy7979 3 DKGDKKKIKNTCPSCNI 19 (186)
Q Consensus 3 ~~~~~~~~~~~CP~C~~ 19 (186)
|.+.++.....||.|+.
T Consensus 12 ~~~~v~~~~~fCP~Cg~ 28 (50)
T PRK00432 12 DGGKVKRKNKFCPRCGS 28 (50)
T ss_pred CCCEEEEccCcCcCCCc
Confidence 33445567789999986
No 74
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=38.51 E-value=8.9 Score=25.36 Aligned_cols=12 Identities=50% Similarity=1.138 Sum_probs=7.2
Q ss_pred CCCCcccccccc
Q psy7979 12 NTCPSCNIIIHQ 23 (186)
Q Consensus 12 ~~CP~C~~~ih~ 23 (186)
.+||.|+..+-+
T Consensus 25 atCP~C~a~~~~ 36 (54)
T PF09237_consen 25 ATCPICGAVIRQ 36 (54)
T ss_dssp EE-TTT--EESS
T ss_pred CCCCcchhhccc
Confidence 689999999844
No 75
>PF08154 NLE: NLE (NUC135) domain; InterPro: IPR012972 This domain is located N-terminal to WD40 repeats(IPR001680 from INTERPRO). It is found in the microtubule-associated protein Q12024 from SWISSPROT [].
Probab=38.37 E-value=1.1e+02 Score=20.50 Aligned_cols=45 Identities=27% Similarity=0.280 Sum_probs=34.1
Q ss_pred ccccEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCC
Q psy7979 111 LKKRFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGK 156 (186)
Q Consensus 111 l~~~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~ 156 (186)
.+..=+-+|+.+|...|...+..-| .+.+.....+++.+|+.|..
T Consensus 15 ~~~~~~~VP~~~t~~~Ls~LvN~LL-~~~~~~vpfdF~i~~~~lr~ 59 (65)
T PF08154_consen 15 VPGTPISVPSNITRKELSELVNQLL-DDEEEPVPFDFLINGEELRT 59 (65)
T ss_pred CCCCCEEEeCCCCHHHHHHHHHHHh-ccCCCCCcEEEEECCEEeec
Confidence 3445678899999999999888766 24455667899999986653
No 76
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=35.83 E-value=27 Score=22.35 Aligned_cols=27 Identities=7% Similarity=0.097 Sum_probs=19.0
Q ss_pred CCCCCcccccccccCCccccccchhHHhhhH
Q psy7979 11 KNTCPSCNIIIHQSHPLQYISFDRTMQDLVY 41 (186)
Q Consensus 11 ~~~CP~C~~~ih~s~Pl~~i~~D~tLQdIVy 41 (186)
+..||.|+..+.. ..+.++..|+..|.
T Consensus 35 ~~~cP~~~~~~~~----~~l~~~~~l~~~i~ 61 (63)
T smart00504 35 HGTDPVTGQPLTH----EDLIPNLALKSAIQ 61 (63)
T ss_pred CCCCCCCcCCCCh----hhceeCHHHHHHHH
Confidence 5689999987732 35677777777653
No 77
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=34.62 E-value=18 Score=22.48 Aligned_cols=12 Identities=25% Similarity=0.971 Sum_probs=9.4
Q ss_pred CCCCCCcccccc
Q psy7979 10 IKNTCPSCNIII 21 (186)
Q Consensus 10 ~~~~CP~C~~~i 21 (186)
-+.+||.|++.+
T Consensus 16 L~~~Cp~C~~PL 27 (41)
T PF06677_consen 16 LDEHCPDCGTPL 27 (41)
T ss_pred hcCccCCCCCee
Confidence 357899998766
No 78
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=33.93 E-value=1.1e+02 Score=21.25 Aligned_cols=27 Identities=15% Similarity=0.091 Sum_probs=23.0
Q ss_pred EEecccccHHHHHHHHHHHhhcCCCCCce
Q psy7979 116 IRLSSQATITHLKKFVALKLLDEKSKYKE 144 (186)
Q Consensus 116 lrcs~~~tV~hLkKfL~~Kl~~~l~~~~~ 144 (186)
.|.|...||+.||.-|.... +++....
T Consensus 18 kr~~~~~Tv~eLK~kl~~~~--Gi~~~~m 44 (87)
T PF14560_consen 18 KRFPKSITVSELKQKLEKLT--GIPPSDM 44 (87)
T ss_dssp EEEETTSBHHHHHHHHHHHH--TS-TTTE
T ss_pred EEcCCCCCHHHHHHHHHHHh--CCCcccE
Confidence 68899999999999999999 8886644
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=33.64 E-value=1.5e+02 Score=20.03 Aligned_cols=70 Identities=14% Similarity=0.182 Sum_probs=49.3
Q ss_pred cccEEEecccccHHHHHHHHHHHhhcCC-CCCceEEE--Ee--C--CEecCCCCcHHHHHHHhccCCCCCeeEEEeeccc
Q psy7979 112 KKRFIRLSSQATITHLKKFVALKLLDEK-SKYKEIDI--LC--N--DELLGKDHTLKFVYITRWRFRTPPLKLQYRPRID 184 (186)
Q Consensus 112 ~~~ylrcs~~~tV~hLkKfL~~Kl~~~l-~~~~~veI--lc--~--~~~L~~~~TL~~I~~~~W~~~~~Pm~L~Yr~~~~ 184 (186)
..+-|+++...|+..+-+-++.|+ ++ .+..+..+ .. + ..+|+++-....|. ..|.....-.+|..|-+.|
T Consensus 17 ~~k~i~v~~~tTa~evi~~~l~k~--~l~~~~~~y~L~~~~~~~~~er~L~~~E~pl~i~-~~~~~~~~~~~f~lr~~~d 93 (93)
T PF00788_consen 17 TYKTIKVSSSTTAREVIEMALEKF--GLAEDPSDYCLVEVEESGGEERPLDDDECPLQIQ-LQWPKDSQNSRFVLRRKED 93 (93)
T ss_dssp SEEEEEEETTSBHHHHHHHHHHHT--TTSSSGGGEEEEEEECTTTEEEEETTTSBHHHHH-HTTSSGTTTEEEEEEECCC
T ss_pred cEEEEEECCCCCHHHHHHHHHHHh--CCCCCCCCEEEEEEEcCCCEEEEcCCCCchHHHH-HhCccccCceEEEEEEcCC
Confidence 577899999999999999999999 66 33444544 22 2 25888777776665 4787533367777776543
No 80
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=33.19 E-value=15 Score=22.30 Aligned_cols=10 Identities=30% Similarity=1.026 Sum_probs=8.0
Q ss_pred CCCccccccc
Q psy7979 13 TCPSCNIIIH 22 (186)
Q Consensus 13 ~CP~C~~~ih 22 (186)
.||.|+..+.
T Consensus 1 ~CP~C~~~l~ 10 (41)
T PF13453_consen 1 KCPRCGTELE 10 (41)
T ss_pred CcCCCCcccc
Confidence 4999998774
No 81
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.78 E-value=19 Score=25.87 Aligned_cols=22 Identities=18% Similarity=0.401 Sum_probs=14.4
Q ss_pred CCCcccccccccCCccccccchh
Q psy7979 13 TCPSCNIIIHQSHPLQYISFDRT 35 (186)
Q Consensus 13 ~CP~C~~~ih~s~Pl~~i~~D~t 35 (186)
-||.|++.+- ..--.+|..|..
T Consensus 3 lCP~C~v~l~-~~~rs~vEiD~C 24 (88)
T COG3809 3 LCPICGVELV-MSVRSGVEIDYC 24 (88)
T ss_pred ccCcCCceee-eeeecCceeeeC
Confidence 5999999983 444445555543
No 82
>PLN02560 enoyl-CoA reductase
Probab=31.63 E-value=96 Score=27.37 Aligned_cols=47 Identities=19% Similarity=0.167 Sum_probs=34.3
Q ss_pred EEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeC-------CEecCCCCcHHHH
Q psy7979 115 FIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCN-------DELLGKDHTLKFV 163 (186)
Q Consensus 115 ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~-------~~~L~~~~TL~~I 163 (186)
-|.++..+||..||+-|+++- +....++.-+... +..|.++-||.+.
T Consensus 17 ~lev~~~aTV~dLK~~Isk~~--~~~~~~RqRL~~~~~~gk~~g~~L~d~ktL~d~ 70 (308)
T PLN02560 17 GLEVPDSATVADLKKAIHKRK--KKYYPSRQRLTLPLPPGKTRPTVLDDSKSLKDY 70 (308)
T ss_pred eEEcCCCCcHHHHHHHHHHHc--CCCChhheEEEEecCCCCcCccccCCCCCHHhc
Confidence 477899999999999999996 5533445556542 3477888888763
No 83
>PF10407 Cytokin_check_N: Cdc14 phosphatase binding protein N-terminus ; InterPro: IPR018844 Cytokinesis in yeasts involves a family of proteins whose essential function is to bind Cdc14-family phosphatase and prevent this from being sequestered and inhibited in the nucleolus. This is the highly conserved N terminus of a family of proteins which act as cytokinesis checkpoint controls by allowing cells to cope with cytokinesis defects. These proteins are required for rDNA silencing and mini-chromosome maintenance [].
Probab=31.09 E-value=81 Score=22.07 Aligned_cols=52 Identities=25% Similarity=0.378 Sum_probs=38.8
Q ss_pred ccEEEe-cccccHHHHHHHHHHHhhcCCCCCceEEEEe----CCEecCCCCcHHHHH
Q psy7979 113 KRFIRL-SSQATITHLKKFVALKLLDEKSKYKEIDILC----NDELLGKDHTLKFVY 164 (186)
Q Consensus 113 ~~ylrc-s~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc----~~~~L~~~~TL~~I~ 164 (186)
+|||-. .+..|++.|+.=|..|+..--|...+++|.- +|--|+++++..+|-
T Consensus 3 kKFLhlt~~~~tl~~L~~eI~~~f~kLYP~~~~~~I~~LQD~~~cDLD~d~~V~DVf 59 (73)
T PF10407_consen 3 KKFLHLTDPNNTLSQLKEEIEERFKKLYPNEPELEILSLQDSDGCDLDPDFLVKDVF 59 (73)
T ss_pred cEEEEEeCCCCcHHHHHHHHHHHHHHHCCCCCCceEEEeecCCCCCCCcccEeeeee
Confidence 567776 6899999999999999863345555666652 355788888888764
No 84
>cd06408 PB1_NoxR The PB1 domain is present in the Epichloe festucae NoxR protein (NADPH oxidase regulator), a key regulator of NADPH oxidase isoform, NoxA. NoxA is essential for growth control of the fungal endophyte in plant tissue in the process of symbiotic interaction between a fungi and its plant host. The Epichloe festucae p67(phox)-like regulator, NoxR, dispensable in culture but essential in plants for the symbiotic interaction. Plants infected with a noxR deletion mutant show severe stunting and premature senescence, whereas hyphae in the meristematic tissues show increased branching leading to increased fungal colonization of pseudostem and leaf blade tissue. The PB1 domain is a modular domain mediating specific protein-protein interactions which a play role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is
Probab=30.11 E-value=1.2e+02 Score=21.91 Aligned_cols=43 Identities=16% Similarity=0.324 Sum_probs=36.5
Q ss_pred cccEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcH
Q psy7979 112 KKRFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTL 160 (186)
Q Consensus 112 ~~~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL 160 (186)
..+++++|..++...|..=|+.|+ ++. ..+-|-+.++ ++-.||
T Consensus 12 Dv~~i~v~~~i~f~dL~~kIrdkf--~~~--~~~~iKykDE--GD~iti 54 (86)
T cd06408 12 DTRYIMIGPDTGFADFEDKIRDKF--GFK--RRLKIKMKDD--GDMITM 54 (86)
T ss_pred cEEEEEcCCCCCHHHHHHHHHHHh--CCC--CceEEEEEcC--CCCccc
Confidence 467999999999999999999999 665 4777888887 777776
No 85
>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=29.04 E-value=1.5e+02 Score=19.72 Aligned_cols=64 Identities=20% Similarity=0.270 Sum_probs=41.4
Q ss_pred ccEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEe----CC--EecCCCCcHHHHHHHhccCCCCCeeEEEeec
Q psy7979 113 KRFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILC----ND--ELLGKDHTLKFVYITRWRFRTPPLKLQYRPR 182 (186)
Q Consensus 113 ~~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc----~~--~~L~~~~TL~~I~~~~W~~~~~Pm~L~Yr~~ 182 (186)
..=+.++..+|+..|=..|+.++ +|....-.-+.+ +| .-|..+-+|.... .. ...|..|++|++
T Consensus 8 ~~~~~v~~~~t~~~l~~~v~~~l--~l~e~~~FgL~~~~~~~~~~~wL~~~k~l~~q~---~~-~~~~~~l~frvk 77 (80)
T PF09379_consen 8 TKTFEVDPKTTGQDLLEQVCDKL--GLKEKEYFGLQYQVDKDGEHHWLDLDKKLKKQL---KK-NNPPFTLYFRVK 77 (80)
T ss_dssp EEEEEEETTSBHHHHHHHHHHHH--TTSSGGGEEEEE-EBTTSSEEEE-SSSBGGGST---BT-SSSSEEEEEEES
T ss_pred cEEEEEcCCCcHHHHHHHHHHHc--CCCCccEEEEEEeecCCCcceeccCcccHHHHc---CC-CCCCEEEEEEEE
Confidence 44567889999999999999999 777665565555 11 2333344443211 00 246899999876
No 86
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=28.53 E-value=23 Score=24.13 Aligned_cols=16 Identities=25% Similarity=0.723 Sum_probs=13.4
Q ss_pred cCcCCCCCCccccccc
Q psy7979 7 KKKIKNTCPSCNIIIH 22 (186)
Q Consensus 7 ~~~~~~~CP~C~~~ih 22 (186)
-|+...+||.|+..|.
T Consensus 54 ~kd~~H~Cp~C~~~lg 69 (73)
T PF10601_consen 54 CKDVYHYCPNCGAFLG 69 (73)
T ss_pred ccCceEECCCCCCEeE
Confidence 4677899999999985
No 87
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=28.49 E-value=25 Score=23.53 Aligned_cols=17 Identities=24% Similarity=0.737 Sum_probs=13.8
Q ss_pred ccCcCCCCCCccccccc
Q psy7979 6 DKKKIKNTCPSCNIIIH 22 (186)
Q Consensus 6 ~~~~~~~~CP~C~~~ih 22 (186)
+-|+...+||.|+..|.
T Consensus 47 ~~kd~~H~Cp~C~~~lg 63 (67)
T smart00714 47 SFKDVNHYCPNCGAFLG 63 (67)
T ss_pred cccCccEECCCCCCEeE
Confidence 34677899999999885
No 88
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=28.24 E-value=26 Score=20.78 Aligned_cols=10 Identities=30% Similarity=1.089 Sum_probs=6.3
Q ss_pred CCCCcccccc
Q psy7979 12 NTCPSCNIII 21 (186)
Q Consensus 12 ~~CP~C~~~i 21 (186)
..||+|++-+
T Consensus 2 hlcpkcgvgv 11 (36)
T PF09151_consen 2 HLCPKCGVGV 11 (36)
T ss_dssp -B-TTTSSSB
T ss_pred ccCCccCceE
Confidence 3689998866
No 89
>PF07797 DUF1639: Protein of unknown function (DUF1639); InterPro: IPR012438 This approximately 50-residue region is found in a number of sequences derived from hypothetical plant proteins. This region features a highly basic 5 amino-acid stretch towards its centre.
Probab=27.76 E-value=38 Score=22.13 Aligned_cols=23 Identities=22% Similarity=0.261 Sum_probs=19.6
Q ss_pred cccchhHHhhhHhhcccchhhHH
Q psy7979 30 ISFDRTMQDLVYKLVPNLQANEM 52 (186)
Q Consensus 30 i~~D~tLQdIVyKLVPgL~~~E~ 52 (186)
-+..+++|..++.|+||+.-.|.
T Consensus 23 kKRpk~Vqk~ld~lfPG~wL~~v 45 (50)
T PF07797_consen 23 KKRPKNVQKQLDSLFPGLWLSEV 45 (50)
T ss_pred CcccHHHHHHHhhcCcchhhhhc
Confidence 45789999999999999987664
No 90
>PF02597 ThiS: ThiS family; InterPro: IPR003749 ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in Escherichia coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS []. MoaD, a protein involved in sulphur transfer during molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.; PDB: 1JW9_D 1JWB_D 1JWA_D 3BII_D 1NVI_D 1FMA_D 1FM0_D 2QIE_G 2Q5W_D 2K5P_A ....
Probab=27.75 E-value=45 Score=22.14 Aligned_cols=47 Identities=19% Similarity=0.263 Sum_probs=34.9
Q ss_pred ccEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCC---CCcH
Q psy7979 113 KRFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGK---DHTL 160 (186)
Q Consensus 113 ~~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~---~~TL 160 (186)
...+..+...||..|-+.|..++. .+.....+-|++||+.+.+ +.+|
T Consensus 13 ~~~~~~~~~~tv~~ll~~l~~~~p-~~~~~~~~~v~vN~~~v~~~~~~~~l 62 (77)
T PF02597_consen 13 EEEIEVPEGSTVRDLLEALAERYP-ELALRDRVAVAVNGEIVPDDGLDTPL 62 (77)
T ss_dssp EEEEEESSTSBHHHHHHHHCHHTG-GGHTTTTEEEEETTEEEGGGTTTSBE
T ss_pred CeEEecCCCCcHHHHHHHHHhhcc-ccccCccEEEEECCEEcCCccCCcCc
Confidence 345667899999999999999983 2212356778899998887 5555
No 91
>PF11324 DUF3126: Protein of unknown function (DUF3126); InterPro: IPR021473 This family of proteins with unknown function appear to be restricted to Alphaproteobacteria.
Probab=27.52 E-value=1.2e+02 Score=20.81 Aligned_cols=32 Identities=19% Similarity=0.383 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHhhcC-C-----C-CCceEEEEeCCEecC
Q psy7979 124 ITHLKKFVALKLLDE-K-----S-KYKEIDILCNDELLG 155 (186)
Q Consensus 124 V~hLkKfL~~Kl~~~-l-----~-~~~~veIlc~~~~L~ 155 (186)
|.-|+.||+.+|++. | | +...+|++.+++.++
T Consensus 2 i~klq~yLr~~f~n~~i~v~~rpk~~dsaEV~~g~EfiG 40 (63)
T PF11324_consen 2 IKKLQAYLRRTFGNPGITVKARPKKDDSAEVYIGDEFIG 40 (63)
T ss_pred hHHHHHHHHHHhCCCceEEEcCCCCCCceEEEeCCEEEE
Confidence 456899999999311 1 1 135789999887654
No 92
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=27.39 E-value=34 Score=21.29 Aligned_cols=13 Identities=38% Similarity=0.787 Sum_probs=10.1
Q ss_pred CCCCCCccccccc
Q psy7979 10 IKNTCPSCNIIIH 22 (186)
Q Consensus 10 ~~~~CP~C~~~ih 22 (186)
....||.|...|.
T Consensus 36 ~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 36 RKKKCPICRQPIE 48 (50)
T ss_dssp TTSBBTTTTBB-S
T ss_pred cCCCCCcCChhhc
Confidence 5689999999883
No 93
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=27.11 E-value=36 Score=22.59 Aligned_cols=17 Identities=24% Similarity=0.528 Sum_probs=13.3
Q ss_pred cCcCCCCCCcccccccc
Q psy7979 7 KKKIKNTCPSCNIIIHQ 23 (186)
Q Consensus 7 ~~~~~~~CP~C~~~ih~ 23 (186)
..-+|.+||.|+.....
T Consensus 24 ~~~TSq~C~~CG~~~~~ 40 (69)
T PF07282_consen 24 EAYTSQTCPRCGHRNKK 40 (69)
T ss_pred CCCCccCccCccccccc
Confidence 34488999999998854
No 94
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=27.02 E-value=23 Score=22.73 Aligned_cols=10 Identities=30% Similarity=0.886 Sum_probs=5.5
Q ss_pred CCCccccccc
Q psy7979 13 TCPSCNIIIH 22 (186)
Q Consensus 13 ~CP~C~~~ih 22 (186)
.||+|+..+.
T Consensus 22 ~CPlC~r~l~ 31 (54)
T PF04423_consen 22 CCPLCGRPLD 31 (54)
T ss_dssp E-TTT--EE-
T ss_pred cCCCCCCCCC
Confidence 8999998874
No 95
>KOG4248|consensus
Probab=26.81 E-value=81 Score=32.64 Aligned_cols=46 Identities=17% Similarity=0.282 Sum_probs=39.4
Q ss_pred cEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHH
Q psy7979 114 RFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKF 162 (186)
Q Consensus 114 ~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~ 162 (186)
+-+-+-+++||..+|..|+.+. .++++.+= |.|.|.+|.++.+++.
T Consensus 15 ~t~~ig~q~ti~~~~d~~r~~~--ni~s~~qr-~i~~grvl~~~k~vq~ 60 (1143)
T KOG4248|consen 15 RTFIIGAQMTIKEFKDHIRASV--NIPSEKQR-LIYQGRVLQDDKKVQE 60 (1143)
T ss_pred eEEEechHHHHHHHHHHHHHhc--ccccccce-eeecceeeccchhhhh
Confidence 4455679999999999999999 89988665 6788999999998875
No 96
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=26.78 E-value=73 Score=22.55 Aligned_cols=40 Identities=25% Similarity=0.236 Sum_probs=30.2
Q ss_pred EEEecccccHHHHHHHHHHHhhcCCCCCceEE-EEeCCEecCCCCcHH
Q psy7979 115 FIRLSSQATITHLKKFVALKLLDEKSKYKEID-ILCNDELLGKDHTLK 161 (186)
Q Consensus 115 ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~ve-Ilc~~~~L~~~~TL~ 161 (186)
...++..+||.|+ ...| ++| ..+|+ |++||...+-++.++
T Consensus 26 ~~~~~~~~tvkd~----IEsL--GVP-~tEV~~i~vNG~~v~~~~~~~ 66 (81)
T PF14451_consen 26 THPFDGGATVKDV----IESL--GVP-HTEVGLILVNGRPVDFDYRLK 66 (81)
T ss_pred EEecCCCCcHHHH----HHHc--CCC-hHHeEEEEECCEECCCcccCC
Confidence 3567899999985 4566 888 44775 678999998887775
No 97
>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=26.61 E-value=2.2e+02 Score=19.68 Aligned_cols=50 Identities=14% Similarity=0.220 Sum_probs=32.0
Q ss_pred cccEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeC--CE-ecCCCCcHHHH
Q psy7979 112 KKRFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCN--DE-LLGKDHTLKFV 163 (186)
Q Consensus 112 ~~~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~--~~-~L~~~~TL~~I 163 (186)
++--.|.....||..|..|+.... .-+...++++.-+ .. .-..+.||+++
T Consensus 15 ~r~~~rF~~~~tv~~l~~~v~~~~--~~~~~~~f~L~t~fP~k~l~~~~~Tl~ea 67 (79)
T cd01770 15 KRLVQKFNSSHRVSDVRDFIVNAR--PEFAARPFTLMTAFPVKELSDESLTLKEA 67 (79)
T ss_pred CEEEEEeCCCCcHHHHHHHHHHhC--CCCCCCCEEEecCCCCcccCCCCCcHHHC
Confidence 343456678999999999999876 3333456666543 22 22336777764
No 98
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.59 E-value=32 Score=26.01 Aligned_cols=33 Identities=15% Similarity=0.440 Sum_probs=20.1
Q ss_pred ccCcCCCCCCcccccccccCCccccccchhHHhhhHh
Q psy7979 6 DKKKIKNTCPSCNIIIHQSHPLQYISFDRTMQDLVYK 42 (186)
Q Consensus 6 ~~~~~~~~CP~C~~~ih~s~Pl~~i~~D~tLQdIVyK 42 (186)
+..-.+..||.|+..+. + - -+..+..|--++..
T Consensus 44 ~ie~G~t~CP~Cg~~~e-~-~--fvva~~aLVgl~l~ 76 (115)
T COG1885 44 EIEVGSTSCPKCGEPFE-S-A--FVVANTALVGLILS 76 (115)
T ss_pred EEecccccCCCCCCccc-e-e--EEEecceeEEEEEE
Confidence 34456789999998872 1 1 34555555555443
No 99
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=26.39 E-value=36 Score=23.01 Aligned_cols=16 Identities=31% Similarity=0.686 Sum_probs=13.9
Q ss_pred CCCCcccccccccCCc
Q psy7979 12 NTCPSCNIIIHQSHPL 27 (186)
Q Consensus 12 ~~CP~C~~~ih~s~Pl 27 (186)
-.||.|+-...-++|-
T Consensus 18 e~Cp~CG~~t~~~~Pp 33 (59)
T COG2260 18 EKCPVCGGDTKVPHPP 33 (59)
T ss_pred ccCCCCCCccccCCCC
Confidence 5899999998888884
No 100
>PF10588 NADH-G_4Fe-4S_3: NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; InterPro: IPR019574 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry describes the G subunit (one of 14 subunits, A to N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This family does not contain related subunits from formate dehydrogenase complexes. This entry represents the iron-sulphur binding domain of the G subunit.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3M9S_C 2FUG_L 3IAS_L 2YBB_3 3IAM_3 3I9V_3.
Probab=26.25 E-value=51 Score=20.22 Aligned_cols=22 Identities=32% Similarity=0.674 Sum_probs=12.4
Q ss_pred CCCCCcccccccccCCccccccchhHHhhhHhh
Q psy7979 11 KNTCPSCNIIIHQSHPLQYISFDRTMQDLVYKL 43 (186)
Q Consensus 11 ~~~CP~C~~~ih~s~Pl~~i~~D~tLQdIVyKL 43 (186)
...||+|...- +-.||++++.+
T Consensus 13 ~~dC~~C~~~G-----------~CeLQ~~~~~~ 34 (41)
T PF10588_consen 13 PLDCPTCDKNG-----------NCELQDLAYEY 34 (41)
T ss_dssp ---TTT-TTGG-----------G-HHHHHHHHH
T ss_pred CCcCcCCCCCC-----------CCHHHHHHHHh
Confidence 46799998543 56788888764
No 101
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=25.95 E-value=51 Score=22.41 Aligned_cols=29 Identities=10% Similarity=0.088 Sum_probs=18.4
Q ss_pred CCCCCCcccccccccCCccccccchhHHhhhHh
Q psy7979 10 IKNTCPSCNIIIHQSHPLQYISFDRTMQDLVYK 42 (186)
Q Consensus 10 ~~~~CP~C~~~ih~s~Pl~~i~~D~tLQdIVyK 42 (186)
.+..||.|+..+.. ..+.++..|++.|..
T Consensus 38 ~~~~~P~t~~~l~~----~~l~pn~~Lk~~I~~ 66 (73)
T PF04564_consen 38 NGGTDPFTRQPLSE----SDLIPNRALKSAIEE 66 (73)
T ss_dssp TSSB-TTT-SB-SG----GGSEE-HHHHHHHHH
T ss_pred CCCCCCCCCCcCCc----ccceECHHHHHHHHH
Confidence 47899999998853 246788888877754
No 102
>PF11620 GABP-alpha: GA-binding protein alpha chain; InterPro: IPR024668 GA-binding protein alpha is a transcription factor capable of interacting with purine rich repeats (GA repeats). This N-terminal domain found in the transcription factor GABP alpha consists of a five-stranded beta-sheet crossed by a distorted helix and has been termed OST domain. The surface of the GABP alpha OST domain contains two clusters of negatively-charged residues suggesting there are positively-charged partner proteins. The OST domain binds to the CH1 and CH3 domains of the co-activator histone acetyltransferase CBP/p300 [].; PDB: 2JUO_A.
Probab=25.92 E-value=67 Score=23.37 Aligned_cols=40 Identities=20% Similarity=0.247 Sum_probs=27.8
Q ss_pred ccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHH
Q psy7979 120 SQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKF 162 (186)
Q Consensus 120 ~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~ 162 (186)
-+-+++.||+.|-.|+ +++ -..-+|+..|..|.++.||-+
T Consensus 11 I~epl~~Lk~lLe~Rl--~~~-L~~~~f~LQD~~L~~~k~L~d 50 (88)
T PF11620_consen 11 IREPLSTLKKLLERRL--GIS-LSDYEFWLQDIQLEPHKSLVD 50 (88)
T ss_dssp SSSBGGGHHHHSHHHH---S---SS-EEEETTEE--TTSBTTT
T ss_pred cCCcHHHHHHHHHHhh--CCC-cCCCeEEeccceecCCccHHH
Confidence 4557889999999999 544 446678889977999999854
No 103
>COG3716 ManZ Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IID [Carbohydrate transport and metabolism]
Probab=25.66 E-value=30 Score=30.20 Aligned_cols=18 Identities=33% Similarity=0.438 Sum_probs=15.4
Q ss_pred chhHHhhhHhhcccchhh
Q psy7979 33 DRTMQDLVYKLVPNLQAN 50 (186)
Q Consensus 33 D~tLQdIVyKLVPgL~~~ 50 (186)
=.|+||+.+||.|||-.-
T Consensus 216 ~~~~Q~~LD~i~Pgllpl 233 (269)
T COG3716 216 VATVQDILDKIFPGLLPL 233 (269)
T ss_pred eehHHHHHHHHhhhHHHH
Confidence 368999999999999763
No 104
>PF15044 CLU_N: Mitochondrial function, CLU-N-term
Probab=25.25 E-value=1.1e+02 Score=21.12 Aligned_cols=44 Identities=16% Similarity=0.142 Sum_probs=33.3
Q ss_pred cccccHHHHHHHHHHHhhcCCCCCceEEEEeCCEecCCCCcHHHHH
Q psy7979 119 SSQATITHLKKFVALKLLDEKSKYKEIDILCNDELLGKDHTLKFVY 164 (186)
Q Consensus 119 s~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~~~~L~~~~TL~~I~ 164 (186)
+..-+|..|+.+|+..- .---...+.+..+|..|.+.-.|..|-
T Consensus 2 ~~~d~v~dvrq~L~~~~--~t~~~Tn~~L~~~g~~L~~~~el~~i~ 45 (76)
T PF15044_consen 2 SPTDTVQDVRQVLAESP--ETCYLTNFSLEHNGQRLDDFVELSEIE 45 (76)
T ss_pred ChhhHHHHHHHHHHhCc--cccceeEEEEEECCCccCCchhhhhhh
Confidence 56678999999998775 434456788888999988877777663
No 105
>cd00754 MoaD Ubiquitin domain of MoaD-like proteins. MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.
Probab=25.14 E-value=1.1e+02 Score=20.33 Aligned_cols=45 Identities=20% Similarity=0.240 Sum_probs=30.0
Q ss_pred EEecccccHHHHHHHHHHHhhc-CCCCCceEEEEeCCEecCCCCcH
Q psy7979 116 IRLSSQATITHLKKFVALKLLD-EKSKYKEIDILCNDELLGKDHTL 160 (186)
Q Consensus 116 lrcs~~~tV~hLkKfL~~Kl~~-~l~~~~~veIlc~~~~L~~~~TL 160 (186)
+-++...||..|.+.|..++.. .......+-+++||+....+..|
T Consensus 20 ~~~~~~~tv~~ll~~l~~~~~~~~~~~~~~~~v~vNg~~v~~~~~l 65 (80)
T cd00754 20 LELPEGATVGELLDALEARYPGLLEELLARVRIAVNGEYVRLDTPL 65 (80)
T ss_pred EECCCCCcHHHHHHHHHHHCchHHHhhhhcEEEEECCeEcCCCccc
Confidence 4456689999999999988621 00112456688899888755544
No 106
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=25.11 E-value=45 Score=22.21 Aligned_cols=19 Identities=32% Similarity=0.683 Sum_probs=15.0
Q ss_pred CcCCCCCCcccccccccCC
Q psy7979 8 KKIKNTCPSCNIIIHQSHP 26 (186)
Q Consensus 8 ~~~~~~CP~C~~~ih~s~P 26 (186)
+.-+..||-|++..|-|.=
T Consensus 11 ~~v~~~Cp~cGipthcS~e 29 (55)
T PF13824_consen 11 AHVNFECPDCGIPTHCSEE 29 (55)
T ss_pred cccCCcCCCCCCcCccCHH
Confidence 3567899999999987643
No 107
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.28 E-value=53 Score=30.21 Aligned_cols=28 Identities=18% Similarity=0.393 Sum_probs=22.5
Q ss_pred CCCCcccccccccCCccccccchhHHhhhHhh
Q psy7979 12 NTCPSCNIIIHQSHPLQYISFDRTMQDLVYKL 43 (186)
Q Consensus 12 ~~CP~C~~~ih~s~Pl~~i~~D~tLQdIVyKL 43 (186)
..||+|...+... .++.+..|.+||..+
T Consensus 61 ~~CP~Cr~~~~~~----~Lr~N~~L~~iVe~~ 88 (397)
T TIGR00599 61 PKCPLCRAEDQES----KLRSNWLVSEIVESF 88 (397)
T ss_pred CCCCCCCCccccc----cCccchHHHHHHHHH
Confidence 4799999998432 678999999999754
No 108
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=23.22 E-value=40 Score=20.99 Aligned_cols=11 Identities=27% Similarity=0.908 Sum_probs=7.7
Q ss_pred CCCCccccccc
Q psy7979 12 NTCPSCNIIIH 22 (186)
Q Consensus 12 ~~CP~C~~~ih 22 (186)
++||.|+..+.
T Consensus 1 ~FCp~Cg~~l~ 11 (52)
T smart00661 1 KFCPKCGNMLI 11 (52)
T ss_pred CCCCCCCCccc
Confidence 36888877663
No 109
>KOG3109|consensus
Probab=23.22 E-value=43 Score=28.69 Aligned_cols=25 Identities=28% Similarity=0.473 Sum_probs=22.0
Q ss_pred ccccccCCccccccchhHHhhhHhh
Q psy7979 19 IIIHQSHPLQYISFDRTMQDLVYKL 43 (186)
Q Consensus 19 ~~ih~s~Pl~~i~~D~tLQdIVyKL 43 (186)
..||++-|+++|+||..|.++.-+|
T Consensus 88 ~~V~~~LPlq~LkPD~~LRnlLL~l 112 (244)
T KOG3109|consen 88 RFVHGRLPLQDLKPDPVLRNLLLSL 112 (244)
T ss_pred HHhhccCcHhhcCCCHHHHHHHHhC
Confidence 4589999999999999999987665
No 110
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=22.88 E-value=48 Score=23.42 Aligned_cols=24 Identities=8% Similarity=0.070 Sum_probs=16.0
Q ss_pred cCCCCCCcccccccccCCccccccch
Q psy7979 9 KIKNTCPSCNIIIHQSHPLQYISFDR 34 (186)
Q Consensus 9 ~~~~~CP~C~~~ih~s~Pl~~i~~D~ 34 (186)
+.+..|++|+..|.. .+ ..+-||.
T Consensus 76 ~~~~~C~vC~k~l~~-~~-f~~~p~~ 99 (109)
T PF10367_consen 76 TESTKCSVCGKPLGN-SV-FVVFPCG 99 (109)
T ss_pred CCCCCccCcCCcCCC-ce-EEEeCCC
Confidence 456889999999954 33 3444543
No 111
>COG0267 RpmG Ribosomal protein L33 [Translation, ribosomal structure and biogenesis]
Probab=22.43 E-value=30 Score=22.56 Aligned_cols=16 Identities=25% Similarity=0.717 Sum_probs=11.6
Q ss_pred ccCcCCCCCCcccccc
Q psy7979 6 DKKKIKNTCPSCNIII 21 (186)
Q Consensus 6 ~~~~~~~~CP~C~~~i 21 (186)
++-+-.++||+|+..+
T Consensus 29 ~rLelkKycp~~~kht 44 (50)
T COG0267 29 ERLELKKYCPVCRKHT 44 (50)
T ss_pred ceEEEEecCcccccEE
Confidence 3345569999999864
No 112
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=22.31 E-value=32 Score=26.84 Aligned_cols=12 Identities=25% Similarity=0.933 Sum_probs=8.5
Q ss_pred CCCCCCcccccc
Q psy7979 10 IKNTCPSCNIII 21 (186)
Q Consensus 10 ~~~~CP~C~~~i 21 (186)
.+.+||.|+..+
T Consensus 27 L~~hCp~Cg~PL 38 (131)
T COG1645 27 LAKHCPKCGTPL 38 (131)
T ss_pred HHhhCcccCCcc
Confidence 356788887765
No 113
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=22.15 E-value=55 Score=18.95 Aligned_cols=11 Identities=27% Similarity=0.655 Sum_probs=8.7
Q ss_pred CCCCCCccccc
Q psy7979 10 IKNTCPSCNII 20 (186)
Q Consensus 10 ~~~~CP~C~~~ 20 (186)
..-.||+|+..
T Consensus 16 ~~~~CP~Cg~~ 26 (33)
T cd00350 16 APWVCPVCGAP 26 (33)
T ss_pred CCCcCcCCCCc
Confidence 56799999863
No 114
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=22.06 E-value=48 Score=18.97 Aligned_cols=13 Identities=15% Similarity=0.363 Sum_probs=7.5
Q ss_pred CCCCCCccccccc
Q psy7979 10 IKNTCPSCNIIIH 22 (186)
Q Consensus 10 ~~~~CP~C~~~ih 22 (186)
++.+||.|+....
T Consensus 2 ~~rfC~~CG~~t~ 14 (32)
T PF09297_consen 2 NHRFCGRCGAPTK 14 (32)
T ss_dssp TTSB-TTT--BEE
T ss_pred CCcccCcCCcccc
Confidence 4688999988764
No 115
>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=21.65 E-value=3.9e+02 Score=20.69 Aligned_cols=63 Identities=22% Similarity=0.214 Sum_probs=41.9
Q ss_pred ccEEEecccccHHHHHHHHHHHhhcCCCCCceEEEEeC--C----EecCCCCcHHHHHHHhccCCCCCeeEEEeec
Q psy7979 113 KRFIRLSSQATITHLKKFVALKLLDEKSKYKEIDILCN--D----ELLGKDHTLKFVYITRWRFRTPPLKLQYRPR 182 (186)
Q Consensus 113 ~~ylrcs~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc~--~----~~L~~~~TL~~I~~~~W~~~~~Pm~L~Yr~~ 182 (186)
..-+.+....||..+-..++.++ ++......=++.- + ..|....+|.++.. .| .+..|.||++
T Consensus 15 ~~~~~~~~~~t~~ev~~~v~~~~--~l~~~~~F~L~~~~~~~~~~~~l~~~~~l~~~~~-~~----~~~~l~fr~r 83 (207)
T smart00295 15 TLEFEVDSSTTAEELLETVCRKL--GIRESEYFGLQFEDPDEDLSHWLDPAKTLLDQDV-KS----EPLTLYFRVK 83 (207)
T ss_pred EEEEEECCCCCHHHHHHHHHHHh--CCCccceeEEEEEcCCCCcCeeCCCccCHHHhcC-CC----CCcEEEEEEE
Confidence 44688889999999999999999 7764444444431 1 35666667666531 11 4667777765
No 116
>smart00746 TRASH metallochaperone-like domain.
Probab=21.52 E-value=48 Score=17.54 Aligned_cols=9 Identities=33% Similarity=0.626 Sum_probs=8.1
Q ss_pred CCccccccc
Q psy7979 14 CPSCNIIIH 22 (186)
Q Consensus 14 CP~C~~~ih 22 (186)
||.|+..|.
T Consensus 1 c~~C~~~~~ 9 (39)
T smart00746 1 CSFCGKDIY 9 (39)
T ss_pred CCCCCCCcc
Confidence 899999996
No 117
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=21.40 E-value=39 Score=20.07 Aligned_cols=11 Identities=27% Similarity=0.905 Sum_probs=7.9
Q ss_pred CCCCccccccc
Q psy7979 12 NTCPSCNIIIH 22 (186)
Q Consensus 12 ~~CP~C~~~ih 22 (186)
.+||.|+..+.
T Consensus 2 ~FCp~C~nlL~ 12 (35)
T PF02150_consen 2 RFCPECGNLLY 12 (35)
T ss_dssp -BETTTTSBEE
T ss_pred eeCCCCCccce
Confidence 47999988773
No 118
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=20.84 E-value=51 Score=22.39 Aligned_cols=38 Identities=24% Similarity=0.491 Sum_probs=23.0
Q ss_pred CCCCCCcccccccccCCccccccchhHHhhhHhhcccchhhHHHHHHHHH
Q psy7979 10 IKNTCPSCNIIIHQSHPLQYISFDRTMQDLVYKLVPNLQANEMKREREFY 59 (186)
Q Consensus 10 ~~~~CP~C~~~ih~s~Pl~~i~~D~tLQdIVyKLVPgL~~~E~~rr~eFy 59 (186)
..++||+|+..|- |=+..=+|+. |+|. ..|.+|.+.|.
T Consensus 7 PH~HC~VCg~aIp---~de~~CSe~C-~eil--------~ker~R~r~~~ 44 (64)
T COG4068 7 PHRHCVVCGKAIP---PDEQVCSEEC-GEIL--------NKERKRQRNFM 44 (64)
T ss_pred CCccccccCCcCC---CccchHHHHH-HHHH--------HHHHHHHHHHH
Confidence 4689999999883 2223344443 4454 34666666554
No 119
>PF08783 DWNN: DWNN domain; InterPro: IPR014891 The ~75-residue DWNN (Domain With No Name) domain is highly conserved through eukaryotic species but is absent in prokaryotes. The DWNN domain is found only at the N terminus of the RBBP6 family of proteins which includes: Mammalian RBBP6, a splicing-associated protein that plays a role in the induction of apoptosis and regulation of the cell cycle. Drosophila melanogaster (Fruit fly) SNAMA (something that sticks like glue), a protein that appears to play a role in apoptosis. All of the identified RBBP6 homologues include the DWNN domain, a CCHC-type zinc finger (see PDOC50158 from PROSITEDOC) and a RING-type zinc finger (see PDOC00449 from PROSITEDOC). The three domain form is found in plants, protozoa, fungi and microsporidia. The RBBP6 homologues in vertebrates, insects and worms are longer and include additional domains. In addition to forming part of the full-length RBBP6 protein, the DWNN domain is also expressed in vertebrates as a small protein containing a DWNN domain and a short C-terminal tail (RBBP6 variant 3). The DWNN domain adopts a fold similar to the ubiquitin one, characterised by two alpha-helices and four beta-sheets ordered as beta-beta-alpha-beta-alpha-beta along the sequence. The similarity of DWNN domain to ubiquitin and the presence of the RING finger suggest that the DWNN domain may act as an ubiquitin-like modifier, possibly playing a role in the regulation of the splicing machinery [, ]. ; GO: 0008270 zinc ion binding, 0005634 nucleus; PDB: 2C7H_A.
Probab=20.43 E-value=1.5e+02 Score=20.69 Aligned_cols=28 Identities=18% Similarity=0.252 Sum_probs=19.7
Q ss_pred ccccHHHHHHHHHHHhhcCCCCCceEEEEe
Q psy7979 120 SQATITHLKKFVALKLLDEKSKYKEIDILC 149 (186)
Q Consensus 120 ~~~tV~hLkKfL~~Kl~~~l~~~~~veIlc 149 (186)
..++|+.||+-|+.+- .++.....|+..
T Consensus 19 ~~Isv~dLKr~I~~~~--~lg~~~dfdL~i 46 (74)
T PF08783_consen 19 TSISVFDLKREIIEKK--KLGKGTDFDLVI 46 (74)
T ss_dssp SEEEHHHHHHHHHHHH--T---TTTEEEEE
T ss_pred CeeEHHHHHHHHHHHh--CCCcCCcCCEEE
Confidence 6789999999999887 666555565544
No 120
>KOG2015|consensus
Probab=20.24 E-value=75 Score=28.98 Aligned_cols=34 Identities=26% Similarity=0.521 Sum_probs=25.3
Q ss_pred cCCCCCCcccccccccCCccccccchhHHhhhHhhccc
Q psy7979 9 KIKNTCPSCNIIIHQSHPLQYISFDRTMQDLVYKLVPN 46 (186)
Q Consensus 9 ~~~~~CP~C~~~ih~s~Pl~~i~~D~tLQdIVyKLVPg 46 (186)
+....||+|.... +.-+ |.+--||||++.-|-+.
T Consensus 326 er~~nC~vCS~~~-~~~~---ispt~tl~~vl~~ls~~ 359 (422)
T KOG2015|consen 326 ERDKNCPVCSNLV-QNYD---ISPTVTLEDVLNHLSKS 359 (422)
T ss_pred ccCCCCccccCCC-cccc---cCCcccHHHHHHHhhhh
Confidence 3457899999887 3333 56899999999877643
No 121
>PRK00420 hypothetical protein; Validated
Probab=20.23 E-value=48 Score=25.16 Aligned_cols=16 Identities=19% Similarity=0.252 Sum_probs=11.0
Q ss_pred CcCCCCCCcccccccc
Q psy7979 8 KKIKNTCPSCNIIIHQ 23 (186)
Q Consensus 8 ~~~~~~CP~C~~~ih~ 23 (186)
+....+||.|+..+--
T Consensus 37 k~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 37 KDGEVVCPVHGKVYIV 52 (112)
T ss_pred CCCceECCCCCCeeee
Confidence 4566788888877643
No 122
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=20.05 E-value=73 Score=21.69 Aligned_cols=12 Identities=33% Similarity=0.924 Sum_probs=9.8
Q ss_pred CCCCCCcccccc
Q psy7979 10 IKNTCPSCNIII 21 (186)
Q Consensus 10 ~~~~CP~C~~~i 21 (186)
..-.||+|+..+
T Consensus 5 ~~v~CP~C~k~~ 16 (62)
T PRK00418 5 ITVNCPTCGKPV 16 (62)
T ss_pred ccccCCCCCCcc
Confidence 456899999986
Done!