Query psy11813
Match_columns 70
No_of_seqs 114 out of 447
Neff 6.4
Searched_HMMs 46136
Date Fri Aug 16 19:39:57 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11813.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11813hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3530|consensus 99.9 1.6E-22 3.5E-27 151.7 4.5 65 2-66 8-73 (616)
2 PF09379 FERM_N: FERM N-termin 99.8 2.3E-21 5E-26 111.9 5.2 59 9-67 1-61 (80)
3 KOG3527|consensus 99.8 1.7E-19 3.7E-24 139.8 3.8 67 2-68 29-96 (975)
4 KOG3531|consensus 99.7 9.8E-18 2.1E-22 130.0 5.4 65 2-66 37-102 (1036)
5 KOG3529|consensus 99.6 4.8E-17 1E-21 123.1 1.0 67 1-67 10-76 (596)
6 KOG0792|consensus 99.4 1.3E-13 2.7E-18 109.1 4.2 64 4-67 22-87 (1144)
7 smart00295 B41 Band 4.1 homolo 99.3 9.8E-12 2.1E-16 80.6 7.0 66 2-67 1-68 (207)
8 cd01777 SNX27_RA Ubiquitin dom 97.2 0.00044 9.5E-09 41.6 3.3 48 5-52 2-52 (87)
9 cd06407 PB1_NLP A PB1 domain i 96.6 0.011 2.4E-07 34.8 5.8 53 5-57 1-53 (82)
10 PF11543 UN_NPL4: Nuclear pore 95.1 0.047 1E-06 31.9 3.9 42 1-42 1-42 (80)
11 smart00666 PB1 PB1 domain. Pho 94.5 0.23 4.9E-06 28.0 5.7 49 5-55 2-51 (81)
12 cd06396 PB1_NBR1 The PB1 domai 94.4 0.26 5.5E-06 29.2 5.9 51 6-59 2-54 (81)
13 PF11976 Rad60-SLD: Ubiquitin- 94.3 0.14 3.1E-06 28.3 4.4 46 5-50 1-47 (72)
14 cd06408 PB1_NoxR The PB1 domai 94.3 0.31 6.7E-06 29.2 6.0 49 4-55 2-50 (86)
15 cd06397 PB1_UP1 Uncharacterize 93.3 0.3 6.6E-06 29.0 4.7 51 6-57 2-52 (82)
16 cd06398 PB1_Joka2 The PB1 doma 93.2 0.52 1.1E-05 28.2 5.8 54 6-59 2-60 (91)
17 cd01763 Sumo Small ubiquitin-r 93.1 0.45 9.7E-06 27.7 5.3 40 2-41 9-49 (87)
18 PF00788 RA: Ras association ( 93.0 0.81 1.8E-05 25.9 6.3 55 5-59 3-64 (93)
19 cd05992 PB1 The PB1 domain is 92.2 0.85 1.8E-05 25.4 5.5 49 6-55 2-51 (81)
20 cd01806 Nedd8 Nebb8-like ubiq 91.9 0.49 1.1E-05 26.0 4.2 38 5-42 1-39 (76)
21 PF00564 PB1: PB1 domain; Int 91.2 1.3 2.7E-05 24.9 5.6 52 4-56 1-53 (84)
22 PF11470 TUG-UBL1: GLUT4 regul 90.9 0.3 6.6E-06 27.6 2.7 49 12-66 4-53 (65)
23 cd06409 PB1_MUG70 The MUG70 pr 90.1 1.4 3.1E-05 26.2 5.2 49 11-59 7-58 (86)
24 cd01768 RA RA (Ras-associating 90.1 1.6 3.5E-05 24.8 5.4 47 7-53 2-53 (87)
25 PF00789 UBX: UBX domain; Int 90.0 1.3 2.7E-05 25.0 4.8 47 3-49 5-52 (82)
26 smart00213 UBQ Ubiquitin homol 89.9 0.98 2.1E-05 23.6 4.1 44 5-49 1-44 (64)
27 PF02196 RBD: Raf-like Ras-bin 89.4 1.7 3.6E-05 24.7 5.0 38 6-43 2-40 (71)
28 smart00455 RBD Raf-like Ras-bi 88.6 2 4.2E-05 24.4 4.9 44 6-50 1-45 (70)
29 cd01760 RBD Ubiquitin-like dom 88.2 1 2.2E-05 25.9 3.5 44 6-50 1-45 (72)
30 cd01809 Scythe_N Ubiquitin-lik 88.1 1.6 3.4E-05 23.7 4.2 44 5-49 1-45 (72)
31 smart00314 RA Ras association 87.4 3.8 8.3E-05 23.4 6.2 47 5-51 3-54 (90)
32 cd06406 PB1_P67 A PB1 domain i 86.0 3.7 8E-05 24.2 5.1 47 5-53 3-49 (80)
33 cd01792 ISG15_repeat1 ISG15 ub 85.8 2.8 6.1E-05 23.7 4.5 35 5-39 3-38 (80)
34 cd01807 GDX_N ubiquitin-like d 85.5 2.6 5.6E-05 23.4 4.2 38 5-42 1-39 (74)
35 cd01787 GRB7_RA RA (RAS-associ 84.3 3.8 8.2E-05 24.5 4.7 45 4-48 2-47 (85)
36 KOG3784|consensus 84.2 2.1 4.5E-05 32.1 4.2 47 5-51 108-157 (407)
37 cd01805 RAD23_N Ubiquitin-like 83.1 4 8.7E-05 22.5 4.3 35 5-39 1-36 (77)
38 KOG3531|consensus 82.6 0.05 1.1E-06 44.0 -4.9 62 4-65 177-239 (1036)
39 PTZ00044 ubiquitin; Provisiona 82.2 4.2 9.1E-05 22.4 4.2 37 5-41 1-38 (76)
40 cd01803 Ubiquitin Ubiquitin. U 82.2 4.1 8.9E-05 22.2 4.1 36 5-40 1-37 (76)
41 cd01775 CYR1_RA Ubiquitin doma 78.2 13 0.00028 22.7 5.6 62 4-65 2-64 (97)
42 PF13019 Telomere_Sde2: Telome 76.9 9.7 0.00021 25.2 5.2 46 5-50 1-51 (162)
43 cd01804 midnolin_N Ubiquitin-l 76.2 10 0.00022 21.4 4.6 35 5-39 2-37 (78)
44 TIGR01961 NuoC_fam NADH (or F4 70.0 2.6 5.7E-05 25.7 1.2 33 30-62 71-106 (121)
45 cd01817 RGS12_RBD Ubiquitin do 69.5 11 0.00025 21.8 3.7 35 6-40 1-36 (73)
46 cd01818 TIAM1_RBD Ubiquitin do 67.5 9.5 0.00021 22.4 3.1 43 8-50 3-47 (77)
47 PRK12494 NADH dehydrogenase su 67.1 2.6 5.7E-05 27.8 0.8 33 30-62 114-149 (172)
48 cd01802 AN1_N ubiquitin-like d 65.8 22 0.00049 21.3 4.7 38 3-40 26-64 (103)
49 cd01812 BAG1_N Ubiquitin-like 65.0 20 0.00043 19.2 4.2 36 5-40 1-36 (71)
50 cd06404 PB1_aPKC PB1 domain is 61.6 32 0.00069 20.4 5.5 53 7-59 3-55 (83)
51 cd01798 parkin_N amino-termina 60.6 19 0.00042 19.5 3.5 35 8-42 2-37 (70)
52 cd00196 UBQ Ubiquitin-like pro 59.3 13 0.00027 17.6 2.4 40 9-49 2-42 (69)
53 cd00419 Ferrochelatase_C Ferro 57.1 13 0.00029 23.2 2.7 34 28-62 45-78 (135)
54 cd01776 Rin1_RA Ubiquitin doma 56.2 42 0.00091 20.1 4.7 53 7-60 2-59 (87)
55 cd01769 UBL Ubiquitin-like dom 56.0 27 0.00057 18.1 3.4 40 9-49 2-42 (69)
56 PF14847 Ras_bdg_2: Ras-bindin 55.4 28 0.0006 21.3 3.8 36 6-41 2-38 (105)
57 PRK07735 NADH dehydrogenase su 55.2 4.4 9.5E-05 30.7 0.2 32 31-62 378-412 (430)
58 KOG0005|consensus 54.6 29 0.00063 19.8 3.5 46 5-50 1-51 (70)
59 cd01813 UBP_N UBP ubiquitin pr 54.5 35 0.00076 19.1 3.9 35 6-40 2-36 (74)
60 PRK06074 NADH dehydrogenase su 53.5 6.4 0.00014 26.3 0.8 33 31-63 102-137 (189)
61 smart00166 UBX Domain present 51.9 42 0.0009 18.8 4.9 45 3-48 3-48 (80)
62 cd01808 hPLIC_N Ubiquitin-like 50.7 40 0.00087 18.3 4.0 43 6-49 2-44 (71)
63 cd06401 PB1_TFG The PB1 domain 50.1 52 0.0011 19.4 5.1 50 7-56 3-55 (81)
64 cd01791 Ubl5 UBL5 ubiquitin-li 48.0 49 0.0011 18.5 4.3 35 5-39 2-37 (73)
65 PRK15031 5-carboxymethyl-2-hyd 47.9 12 0.00025 23.7 1.3 29 21-49 76-105 (126)
66 PF00240 ubiquitin: Ubiquitin 47.6 38 0.00083 17.9 3.2 30 11-40 2-32 (69)
67 CHL00012 ndhJ NADH dehydrogena 45.2 8.6 0.00019 25.3 0.4 32 31-62 101-135 (158)
68 cd01810 ISG15_repeat2 ISG15 ub 44.8 48 0.001 18.1 3.4 33 8-40 2-35 (74)
69 COG5227 SMT3 Ubiquitin-like pr 44.0 50 0.0011 20.3 3.6 35 4-38 24-59 (103)
70 PF06100 Strep_67kDa_ant: Stre 43.5 13 0.00029 28.6 1.2 21 23-43 409-429 (500)
71 KOG4261|consensus 42.7 16 0.00035 30.1 1.6 47 3-49 83-130 (1003)
72 cd01767 UBX UBX (ubiquitin reg 42.1 61 0.0013 17.9 5.3 43 5-49 3-46 (77)
73 cd01772 SAKS1_UBX SAKS1-like U 39.7 71 0.0015 18.0 4.8 36 3-38 3-39 (79)
74 PF01337 Barstar: Barstar (bar 39.7 23 0.0005 20.2 1.6 27 18-46 3-29 (90)
75 cd01770 p47_UBX p47-like ubiqu 39.2 75 0.0016 18.1 5.4 46 4-49 4-50 (79)
76 cd01774 Faf1_like2_UBX Faf1 ik 38.5 81 0.0017 18.2 4.9 45 3-49 3-48 (85)
77 KOG2378|consensus 38.5 1.5E+02 0.0032 23.3 6.1 58 4-63 235-293 (573)
78 cd01794 DC_UbP_C dendritic cel 37.7 73 0.0016 17.5 3.7 33 8-40 2-35 (70)
79 COG3232 HpaF 5-carboxymethyl-2 37.2 14 0.0003 23.7 0.4 30 21-50 76-106 (127)
80 PF00329 Complex1_30kDa: Respi 37.1 7.4 0.00016 23.1 -0.8 20 43-62 75-94 (103)
81 PRK13977 myosin-cross-reactive 36.8 19 0.00042 28.1 1.2 19 23-41 427-445 (576)
82 PF02962 CHMI: 5-carboxymethyl 36.8 17 0.00036 22.9 0.7 29 21-49 75-104 (124)
83 PRK07785 NADH dehydrogenase su 35.2 18 0.0004 25.2 0.8 31 31-61 166-199 (235)
84 smart00460 TGc Transglutaminas 33.9 64 0.0014 16.7 2.8 34 27-60 13-54 (68)
85 KOG1769|consensus 33.8 1.2E+02 0.0025 18.7 4.5 38 3-40 19-57 (99)
86 PF00762 Ferrochelatase: Ferro 33.2 43 0.00093 23.9 2.4 31 29-62 212-242 (316)
87 cd02639 R3H_RRM R3H domain of 32.2 44 0.00096 18.4 1.9 27 17-43 19-47 (60)
88 PRK12435 ferrochelatase; Provi 31.2 48 0.001 23.7 2.4 30 30-62 203-233 (311)
89 cd06411 PB1_p51 The PB1 domain 30.0 1.2E+02 0.0026 17.7 3.8 45 17-62 10-54 (78)
90 PRK08491 NADH dehydrogenase su 29.5 25 0.00055 24.9 0.8 32 31-62 129-163 (263)
91 cd01796 DDI1_N DNA damage indu 29.3 1E+02 0.0023 16.7 3.7 35 8-42 2-38 (71)
92 cd01797 NIRF_N amino-terminal 28.5 1.2E+02 0.0025 17.1 3.8 44 5-49 1-47 (78)
93 cd01771 Faf1_UBX Faf1 UBX doma 28.2 1.2E+02 0.0027 17.2 4.3 43 4-48 4-47 (80)
94 TIGR00601 rad23 UV excision re 27.1 1.3E+02 0.0028 22.3 4.1 34 5-38 1-35 (378)
95 PF14533 USP7_C2: Ubiquitin-sp 26.2 56 0.0012 21.9 2.0 37 6-42 20-62 (213)
96 cd06403 PB1_Par6 The PB1 domai 25.9 1.5E+02 0.0033 17.5 3.8 43 13-55 8-52 (80)
97 cd01800 SF3a120_C Ubiquitin-li 25.8 1.2E+02 0.0026 16.6 3.0 29 12-40 5-34 (76)
98 PF07865 DUF1652: Protein of u 25.8 59 0.0013 18.5 1.7 25 4-28 14-39 (69)
99 PF14039 YusW: YusW-like prote 25.7 36 0.00077 20.3 0.8 30 18-47 56-86 (92)
100 cd03590 CLECT_DC-SIGN_like C-t 25.2 1E+02 0.0022 17.7 2.8 33 31-63 46-78 (126)
101 PF15152 Kisspeptin: Kisspepti 25.1 23 0.0005 20.9 -0.1 6 44-49 72-77 (78)
102 TIGR02582 cas_TM1809 CRISPR-as 24.9 55 0.0012 22.0 1.7 22 26-47 172-193 (204)
103 COG0276 HemH Protoheme ferro-l 24.7 83 0.0018 22.9 2.7 35 27-62 210-244 (320)
104 cd05141 Barstar_evA4336-like B 24.3 68 0.0015 18.2 1.8 26 19-46 4-29 (81)
105 PF01841 Transglut_core: Trans 24.2 58 0.0013 18.5 1.6 24 27-50 58-81 (113)
106 PRK11615 hypothetical protein; 24.1 70 0.0015 21.7 2.1 19 7-25 41-59 (185)
107 PF13718 GNAT_acetyltr_2: GNAT 23.2 78 0.0017 21.4 2.2 30 21-50 103-157 (196)
108 cd07762 CYTH-like_Pase_1 Uncha 22.7 1E+02 0.0022 20.1 2.6 25 16-40 144-168 (180)
109 COG5605 Predicted small integr 22.7 14 0.00031 22.8 -1.3 7 42-48 39-45 (115)
110 PF12380 Peptidase_C62: Gill-a 22.5 94 0.002 21.6 2.5 44 23-70 144-188 (284)
111 cd06901 lectin_VIP36_VIPL VIP3 21.7 1.2E+02 0.0026 21.0 3.0 44 6-51 161-206 (248)
112 PF00794 PI3K_rbd: PI3-kinase 21.7 1.8E+02 0.004 17.0 5.3 48 3-50 15-69 (106)
113 PRK11742 bifunctional NADH:ubi 21.0 46 0.001 25.9 0.8 32 31-62 104-138 (575)
114 PLN02560 enoyl-CoA reductase 20.8 3.3E+02 0.0071 19.5 5.2 46 5-50 1-50 (308)
115 cd01783 DAGK_delta_RA Ubiquiti 20.7 1.1E+02 0.0024 18.6 2.3 35 16-50 19-55 (97)
116 KOG4360|consensus 20.6 25 0.00055 27.6 -0.6 35 30-64 504-538 (596)
No 1
>KOG3530|consensus
Probab=99.86 E-value=1.6e-22 Score=151.72 Aligned_cols=65 Identities=28% Similarity=0.481 Sum_probs=61.9
Q ss_pred CceEEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCceeeeeeeEEEecCCCCeecccCCCeec
Q psy11813 2 NGLMNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYADSRGDLTWIKLYKKVR 66 (70)
Q Consensus 2 ~~~~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y~d~~~~~~WLd~~k~i~ 66 (70)
++.+.|+|.|||| .+.++++++++|++|||.||.+|+|+|+|||||+|+|..++.+|||+.|+|+
T Consensus 8 k~~~~C~V~LLd~sdl~~~~pk~akGq~Lld~V~~~ldl~E~DYFGLry~D~~~~~hWLD~tK~I~ 73 (616)
T KOG3530|consen 8 KKDVYCRVLLLDGSDLSINFPKTAKGQELLDYVFYHLDLIEKDYFGLRYQDSSKVRHWLDPTKSIK 73 (616)
T ss_pred CcceEEEEEEecCccceeccCcccchHHHHHHHHHhhceeeeeccceeeechhhcceecCcchhHH
Confidence 4678999999999 7888899999999999999999999999999999999999999999999985
No 2
>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=99.84 E-value=2.3e-21 Score=111.93 Aligned_cols=59 Identities=37% Similarity=0.729 Sum_probs=55.1
Q ss_pred EEecCC-eEEEEEcccCchhhhHHHHhcccCceeeeeeeEEE-ecCCCCeecccCCCeecC
Q psy11813 9 VTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQY-ADSRGDLTWIKLYKKVRC 67 (70)
Q Consensus 9 V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y-~d~~~~~~WLd~~k~i~~ 67 (70)
|++||| +.+|.++++++|++||++||++|+|.|++||||+| .++++..+||+++|+|..
T Consensus 1 V~llD~~~~~~~v~~~~t~~~l~~~v~~~l~l~e~~~FgL~~~~~~~~~~~wL~~~k~l~~ 61 (80)
T PF09379_consen 1 VRLLDGTTKTFEVDPKTTGQDLLEQVCDKLGLKEKEYFGLQYQVDKDGEHHWLDLDKKLKK 61 (80)
T ss_dssp EEESSEEEEEEEEETTSBHHHHHHHHHHHHTTSSGGGEEEEE-EBTTSSEEEE-SSSBGGG
T ss_pred CCCcCCCcEEEEEcCCCcHHHHHHHHHHHcCCCCccEEEEEEeecCCCcceeccCcccHHH
Confidence 789999 68899999999999999999999999999999999 888999999999999975
No 3
>KOG3527|consensus
Probab=99.77 E-value=1.7e-19 Score=139.82 Aligned_cols=67 Identities=25% Similarity=0.459 Sum_probs=63.2
Q ss_pred CceEEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCceeeeeeeEEEecCCCCeecccCCCeecCC
Q psy11813 2 NGLMNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYADSRGDLTWIKLYKKVRCP 68 (70)
Q Consensus 2 ~~~~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y~d~~~~~~WLd~~k~i~~~ 68 (70)
+|.+.|+|++||+ .++|.++++++|++||+.||+||||+|+|||||.|.++..++.|||+.|+|+.+
T Consensus 29 ~k~~~~~vtlld~s~~~~~~ek~~kg~~~~~~vc~~LnliEkdyfgl~~~~~~~~~~wlD~~k~i~k~ 96 (975)
T KOG3527|consen 29 TKDAICKVTLLDGSEYSCDVEKHAKGQVLFDKVCEHLNLLEKDYFGLTYLTSSEQKNWLDPAKEIKKQ 96 (975)
T ss_pred CCCccceEEEeeCCcceeeeecccccchhHHHHhhccchhhhhhceeEEecCCCCccccccchhhhcc
Confidence 3678999999999 688999999999999999999999999999999999999999999999998754
No 4
>KOG3531|consensus
Probab=99.71 E-value=9.8e-18 Score=130.02 Aligned_cols=65 Identities=29% Similarity=0.558 Sum_probs=61.0
Q ss_pred CceEEEEEEecCCeEE-EEEcccCchhhhHHHHhcccCceeeeeeeEEEecCCCCeecccCCCeec
Q psy11813 2 NGLMNVRVTTMDAELE-FAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYADSRGDLTWIKLYKKVR 66 (70)
Q Consensus 2 ~~~~~~~V~lLD~~~~-~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y~d~~~~~~WLd~~k~i~ 66 (70)
+|...+++.+||++.+ |.|+.+|.|+.||++||+||||.|.|||||.|.|.++.+.|||+.|||.
T Consensus 37 gk~~~~~~~~~~~~~~~f~~~~ka~g~vll~~vc~~lnl~e~dyfglef~~~~~~~~wld~~kpi~ 102 (1036)
T KOG3531|consen 37 GKICFFFCVMLDDTTEVFLVQHKAIGQVLLDQVCRHLNLVECDYFGLEFQDINGNHCWLDLEKPIL 102 (1036)
T ss_pred CceEEEEEEEecCceeEEeecccccchHHHHHHHHhhceeeccccceeeccccCceEEecccchHH
Confidence 5778899999999655 9999999999999999999999999999999999999999999999984
No 5
>KOG3529|consensus
Probab=99.63 E-value=4.8e-17 Score=123.13 Aligned_cols=67 Identities=73% Similarity=1.080 Sum_probs=62.9
Q ss_pred CCceEEEEEEecCCeEEEEEcccCchhhhHHHHhcccCceeeeeeeEEEecCCCCeecccCCCeecC
Q psy11813 1 MNGLMNVRVTTMDAELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYADSRGDLTWIKLYKKVRC 67 (70)
Q Consensus 1 ~~~~~~~~V~lLD~~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y~d~~~~~~WLd~~k~i~~ 67 (70)
|.+.+.|+|+.+|++.+|-++++++|++||++||+++||.|++||||+|+|+.+..+||.++|++..
T Consensus 10 ~~~~~~~rv~~~d~e~~~~i~~~~t~~~l~dlv~~~~glre~~yfgl~~~d~~~~~~wl~~d~~v~~ 76 (596)
T KOG3529|consen 10 MTKPINVRVTTMDAELEFAIQPKTTGKQLFDLVVKTIGLRESWYFGLQYTDSKGEPTWLKLDKKVLD 76 (596)
T ss_pred ccCCcceeeeehhhhhhhhhCcchhHHHHHHHHhccCCCchhhhcccccccCCCCcchhhccchhhh
Confidence 5678999999999966699999999999999999999999999999999999999999999998764
No 6
>KOG0792|consensus
Probab=99.42 E-value=1.3e-13 Score=109.09 Aligned_cols=64 Identities=28% Similarity=0.567 Sum_probs=59.7
Q ss_pred eEEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCceeeeeee-EEEecCCCCeecccCCCeecC
Q psy11813 4 LMNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREVWFFG-LQYADSRGDLTWIKLYKKVRC 67 (70)
Q Consensus 4 ~~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFG-L~y~d~~~~~~WLd~~k~i~~ 67 (70)
.+.|++.+||+ .++|++...++||++++.||++|++.|++||| +.+.++.++.+|||++|+++.
T Consensus 22 ~v~~~i~llds~~~eftls~es~gQ~~ld~V~qrL~~~e~~yFgl~~~~~k~~~~rWvdleK~lkk 87 (1144)
T KOG0792|consen 22 CVVCRILLLDSDVVEFTLSSESTGQELLDAVAQRLELREKEYFGLLWSPDKPDQIRWVDLEKPLKK 87 (1144)
T ss_pred eEEEEEEecCCceEEEEEecCCCchhHHHHHhhhhcccccccccccccCCccCccceeccchhHHH
Confidence 68999999999 78999999999999999999999999999999 667888999999999999863
No 7
>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=99.30 E-value=9.8e-12 Score=80.61 Aligned_cols=66 Identities=30% Similarity=0.581 Sum_probs=59.2
Q ss_pred CceEEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCceeeeeeeEEEecCCCCe-ecccCCCeecC
Q psy11813 2 NGLMNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYADSRGDL-TWIKLYKKVRC 67 (70)
Q Consensus 2 ~~~~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y~d~~~~~-~WLd~~k~i~~ 67 (70)
++.+.++|.++|| ..++.+++.++++++++.||++++|.+..||||.+.+..+.. .|+++.+++..
T Consensus 1 ~~~~~~~V~l~dg~~~~~~~~~~~t~~ev~~~v~~~~~l~~~~~F~L~~~~~~~~~~~~l~~~~~l~~ 68 (207)
T smart00295 1 PKPRVLKVYLLDGTTLEFEVDSSTTAEELLETVCRKLGIRESEYFGLQFEDPDEDLSHWLDPAKTLLD 68 (207)
T ss_pred CCcEEEEEEecCCCEEEEEECCCCCHHHHHHHHHHHhCCCccceeEEEEEcCCCCcCeeCCCccCHHH
Confidence 3678999999999 678999999999999999999999999999999999876555 89999888753
No 8
>cd01777 SNX27_RA Ubiquitin domain of SNX27 (sorting nexin protein 27). SNX27_RA SNX27 (sorting nexin protein 27) belongs to a large family of endosome-localized proteins related to sorting nexin1 which is implicated in regulating membrane traffic. The domain architecture of SNX27 includes an amino-terminal PDZ domain, a PX (PhoX homologous) domain, and a carboxy-terminal RA (RAS-associated) domain.
Probab=97.22 E-value=0.00044 Score=41.58 Aligned_cols=48 Identities=17% Similarity=0.328 Sum_probs=42.2
Q ss_pred EEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCceee--eeeeEEEecC
Q psy11813 5 MNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREV--WFFGLQYADS 52 (70)
Q Consensus 5 ~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~--dYFGL~y~d~ 52 (70)
+..+|.+.|| .+.+++.++.+..++++.||+.++|.+. -||+|--..+
T Consensus 2 V~L~V~Lpdg~~i~V~v~~s~~a~~Vleav~~kl~L~~e~~~YFaLFev~~ 52 (87)
T cd01777 2 VELRIALPDKATVTVRVRKNATTDQVYQALVAKAGMDSYTQNYFALFEVIN 52 (87)
T ss_pred eEEEEEccCCCEEEEEEEEcccHHHHHHHHHHHhCCCHHHHhheeeeEEec
Confidence 5688999999 7899999999999999999999999765 5999976643
No 9
>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=96.63 E-value=0.011 Score=34.81 Aligned_cols=53 Identities=19% Similarity=0.298 Sum_probs=45.4
Q ss_pred EEEEEEecCCeEEEEEcccCchhhhHHHHhcccCceeeeeeeEEEecCCCCee
Q psy11813 5 MNVRVTTMDAELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYADSRGDLT 57 (70)
Q Consensus 5 ~~~~V~lLD~~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y~d~~~~~~ 57 (70)
+.++++.=++.+.|.+++...=++|.+.|.+.+++.+..-|-|.|.|.+|.+.
T Consensus 1 ~~vK~~~~~d~~r~~l~~~~~~~~L~~~i~~r~~~~~~~~f~LkY~Ddegd~v 53 (82)
T cd06407 1 VRVKATYGEEKIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKYLDDDEEWV 53 (82)
T ss_pred CEEEEEeCCeEEEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEEECCCCCeE
Confidence 46777776667889999999999999999999999766789999999887654
No 10
>PF11543 UN_NPL4: Nuclear pore localisation protein NPL4; InterPro: IPR024682 Npl4, along with Ufd1, forms the heterodimer adaptor complex UN, which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway. Npl4 has a N-terminal ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert []. This entry represents the ubiquitin-like domain.; PDB: 2PJH_A 1WF9_A.
Probab=95.10 E-value=0.047 Score=31.88 Aligned_cols=42 Identities=17% Similarity=0.253 Sum_probs=30.0
Q ss_pred CCceEEEEEEecCCeEEEEEcccCchhhhHHHHhcccCceee
Q psy11813 1 MNGLMNVRVTTMDAELEFAIQHTTTGKQLFDQTVKTIGLREV 42 (70)
Q Consensus 1 ~~~~~~~~V~lLD~~~~~~v~~~~~G~~L~d~Vc~~L~L~E~ 42 (70)
|...|.+||+.-||...+++++.++=.+|+++|.+.+++...
T Consensus 1 ~~~~milRvrS~dG~~Rie~~~~~t~~~L~~kI~~~l~~~~~ 42 (80)
T PF11543_consen 1 MASSMILRVRSKDGMKRIEVSPSSTLSDLKEKISEQLSIPDS 42 (80)
T ss_dssp -----EEEEE-SSEEEEEEE-TTSBHHHHHHHHHHHS---TT
T ss_pred CCccEEEEEECCCCCEEEEcCCcccHHHHHHHHHHHcCCCCc
Confidence 678899999999998889999999999999999999998644
No 11
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=94.50 E-value=0.23 Score=28.03 Aligned_cols=49 Identities=22% Similarity=0.411 Sum_probs=40.6
Q ss_pred EEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCceeeeeeeEEEecCCCC
Q psy11813 5 MNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYADSRGD 55 (70)
Q Consensus 5 ~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y~d~~~~ 55 (70)
+.++|.. .+ ...+.+++..+=.+|.++|.+.+++.. .-|.|.|.|.+|.
T Consensus 2 ~~vK~~~-~~~~~~~~~~~~~s~~dL~~~i~~~~~~~~-~~~~l~Y~Dedgd 51 (81)
T smart00666 2 VDVKLRY-GGETRRLSVPRDISFEDLRSKVAKRFGLDN-QSFTLKYQDEDGD 51 (81)
T ss_pred ccEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHhCCCC-CCeEEEEECCCCC
Confidence 4677777 44 566999999999999999999999765 5689999988765
No 12
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, 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. The NBR1 protein contains a type I PB1 domain.
Probab=94.42 E-value=0.26 Score=29.21 Aligned_cols=51 Identities=20% Similarity=0.260 Sum_probs=42.8
Q ss_pred EEEEEecCCeEEEEEcc--cCchhhhHHHHhcccCceeeeeeeEEEecCCCCeecc
Q psy11813 6 NVRVTTMDAELEFAIQH--TTTGKQLFDQTVKTIGLREVWFFGLQYADSRGDLTWI 59 (70)
Q Consensus 6 ~~~V~lLD~~~~~~v~~--~~~G~~L~d~Vc~~L~L~E~dYFGL~y~d~~~~~~WL 59 (70)
+++++.=.+.+.|.+++ ..+=.+|...|-...+|. -|.|.|.|.++.+.=|
T Consensus 2 ~vKaty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~---~f~lKYlDde~e~v~l 54 (81)
T cd06396 2 NLKVTYNGESQSFLVSDSENTTWASVEAMVKVSFGLN---DIQIKYVDEENEEVSV 54 (81)
T ss_pred EEEEEECCeEEEEEecCCCCCCHHHHHHHHHHHhCCC---cceeEEEcCCCCEEEE
Confidence 56777767788999999 668899999999999998 8999999998876543
No 13
>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=94.32 E-value=0.14 Score=28.26 Aligned_cols=46 Identities=22% Similarity=0.390 Sum_probs=39.5
Q ss_pred EEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCceeeeeeeEEEe
Q psy11813 5 MNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYA 50 (70)
Q Consensus 5 ~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y~ 50 (70)
|++.|...++ .+.+.|.++++=+.|++..|+..++....-|-|.|.
T Consensus 1 I~i~v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~fd 47 (72)
T PF11976_consen 1 ITIKVRSQDGKEIKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLIFD 47 (72)
T ss_dssp EEEEEEETTSEEEEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEEET
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCccceEEEEEC
Confidence 5788999999 788999999999999999999999988666677774
No 14
>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=94.25 E-value=0.31 Score=29.16 Aligned_cols=49 Identities=20% Similarity=0.265 Sum_probs=43.5
Q ss_pred eEEEEEEecCCeEEEEEcccCchhhhHHHHhcccCceeeeeeeEEEecCCCC
Q psy11813 4 LMNVRVTTMDAELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYADSRGD 55 (70)
Q Consensus 4 ~~~~~V~lLD~~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y~d~~~~ 55 (70)
.+.++|+.-++..-+.+++...=++|.++|.+.+++. .-|.++|.|. |.
T Consensus 2 ~ikVKv~~~~Dv~~i~v~~~i~f~dL~~kIrdkf~~~--~~~~iKykDE-GD 50 (86)
T cd06408 2 KIRVKVHAQDDTRYIMIGPDTGFADFEDKIRDKFGFK--RRLKIKMKDD-GD 50 (86)
T ss_pred cEEEEEEecCcEEEEEcCCCCCHHHHHHHHHHHhCCC--CceEEEEEcC-CC
Confidence 5788999877788899999999999999999999995 6999999988 53
No 15
>cd06397 PB1_UP1 Uncharacterized protein 1. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a 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 domain, 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.
Probab=93.27 E-value=0.3 Score=29.05 Aligned_cols=51 Identities=16% Similarity=0.213 Sum_probs=39.9
Q ss_pred EEEEEecCCeEEEEEcccCchhhhHHHHhcccCceeeeeeeEEEecCCCCee
Q psy11813 6 NVRVTTMDAELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYADSRGDLT 57 (70)
Q Consensus 6 ~~~V~lLD~~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y~d~~~~~~ 57 (70)
+-+|...++.-.|..+..-+=..|.++++...+|.+-. ||+.|.|.+|...
T Consensus 2 ~fKv~~~g~~RRf~~~~~pt~~~L~~kl~~Lf~lp~~~-~~vtYiDeD~D~I 52 (82)
T cd06397 2 QFKSSFLGDTRRIVFPDIPTWEALASKLENLYNLPEIK-VGVTYIDNDNDEI 52 (82)
T ss_pred eEEEEeCCceEEEecCCCccHHHHHHHHHHHhCCChhH-eEEEEEcCCCCEE
Confidence 45677777766666666666677999999999999876 9999999876544
No 16
>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a 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 domain, 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
Probab=93.21 E-value=0.52 Score=28.18 Aligned_cols=54 Identities=19% Similarity=0.176 Sum_probs=42.7
Q ss_pred EEEEEecCCeEEEEEcc-----cCchhhhHHHHhcccCceeeeeeeEEEecCCCCeecc
Q psy11813 6 NVRVTTMDAELEFAIQH-----TTTGKQLFDQTVKTIGLREVWFFGLQYADSRGDLTWI 59 (70)
Q Consensus 6 ~~~V~lLD~~~~~~v~~-----~~~G~~L~d~Vc~~L~L~E~dYFGL~y~d~~~~~~WL 59 (70)
.++|..=+....|.++. ...-.+|.++|.+.+++..-.-|-|+|.|.++...=|
T Consensus 2 ~vKv~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~Dedgd~V~l 60 (91)
T cd06398 2 VVKVKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVVTL 60 (91)
T ss_pred EEEEEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCEEEE
Confidence 46677644466688875 5788999999999999988788999999987765433
No 17
>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=93.08 E-value=0.45 Score=27.69 Aligned_cols=40 Identities=28% Similarity=0.403 Sum_probs=35.9
Q ss_pred CceEEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCcee
Q psy11813 2 NGLMNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLRE 41 (70)
Q Consensus 2 ~~~~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E 41 (70)
...|+++|..+++ .+.|.|.+.++=+.|+++.|++-++..
T Consensus 9 ~~~i~I~v~~~~g~~~~~~v~~~~~l~~l~~~y~~~~gi~~ 49 (87)
T cd01763 9 SEHINLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQRQGLSM 49 (87)
T ss_pred CCeEEEEEECCCCCEEEEEEcCCCHHHHHHHHHHHHhCCCc
Confidence 3568999999998 789999999999999999999999854
No 18
>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=93.01 E-value=0.81 Score=25.89 Aligned_cols=55 Identities=18% Similarity=0.274 Sum_probs=42.5
Q ss_pred EEEEEEecCCe----E-EEEEcccCchhhhHHHHhcccCc-eeeeeeeEE-EecCCCCeecc
Q psy11813 5 MNVRVTTMDAE----L-EFAIQHTTTGKQLFDQTVKTIGL-REVWFFGLQ-YADSRGDLTWI 59 (70)
Q Consensus 5 ~~~~V~lLD~~----~-~~~v~~~~~G~~L~d~Vc~~L~L-~E~dYFGL~-y~d~~~~~~WL 59 (70)
-.++|..-++. . .+.|.+.++.+++...+++.+++ .+...|.|. +....+..+=|
T Consensus 3 ~~lrVy~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l~~~~~~y~L~~~~~~~~~er~L 64 (93)
T PF00788_consen 3 GVLRVYDGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGLAEDPSDYCLVEVEESGGEERPL 64 (93)
T ss_dssp EEEEEEETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTTSSSGGGEEEEEEECTTTEEEEE
T ss_pred eEEEEEcCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCCCCCCCCEEEEEEEcCCCEEEEc
Confidence 46788888864 5 49999999999999999999999 666789996 54444443333
No 19
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a 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 domain, 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 a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=92.16 E-value=0.85 Score=25.43 Aligned_cols=49 Identities=24% Similarity=0.366 Sum_probs=40.4
Q ss_pred EEEEEecCCeEEEEEc-ccCchhhhHHHHhcccCceeeeeeeEEEecCCCC
Q psy11813 6 NVRVTTMDAELEFAIQ-HTTTGKQLFDQTVKTIGLREVWFFGLQYADSRGD 55 (70)
Q Consensus 6 ~~~V~lLD~~~~~~v~-~~~~G~~L~d~Vc~~L~L~E~dYFGL~y~d~~~~ 55 (70)
.++|+.-++...+.+. ..++=.+|.++|++.+++.. .-|.+.|.|.++.
T Consensus 2 ~vK~~~~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~-~~~~l~y~D~e~d 51 (81)
T cd05992 2 RVKVKYGGEIRRFVVVSRSISFEDLRSKIAEKFGLDA-VSFKLKYPDEDGD 51 (81)
T ss_pred cEEEEecCCCEEEEEecCCCCHHHHHHHHHHHhCCCC-CcEEEEeeCCCCC
Confidence 4566666667778888 88899999999999999876 6789999998774
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=91.89 E-value=0.49 Score=26.00 Aligned_cols=38 Identities=21% Similarity=0.358 Sum_probs=33.1
Q ss_pred EEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCceee
Q psy11813 5 MNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREV 42 (70)
Q Consensus 5 ~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~ 42 (70)
|.+.|..++| ++++.+++..+-.+|-+++++..++...
T Consensus 1 m~i~v~~~~g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~ 39 (76)
T cd01806 1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQ 39 (76)
T ss_pred CEEEEEeCCCCEEEEEECCCCCHHHHHHHHhHhhCCChh
Confidence 5688999999 7889999999999999999999886433
No 21
>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=91.22 E-value=1.3 Score=24.89 Aligned_cols=52 Identities=23% Similarity=0.258 Sum_probs=43.2
Q ss_pred eEEEEEEecCCeEE-EEEcccCchhhhHHHHhcccCceeeeeeeEEEecCCCCe
Q psy11813 4 LMNVRVTTMDAELE-FAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYADSRGDL 56 (70)
Q Consensus 4 ~~~~~V~lLD~~~~-~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y~d~~~~~ 56 (70)
++.+++..-++... +.+.+..+=.+|.+.|.+.+++. ..=|.|.|.|.+|..
T Consensus 1 t~~vK~~~~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~-~~~~~l~Y~D~dgD~ 53 (84)
T PF00564_consen 1 TVRVKVRYGGDIRRIISLPSDVSFDDLRSKIREKFGLL-DEDFQLKYKDEDGDL 53 (84)
T ss_dssp SEEEEEEETTEEEEEEEECSTSHHHHHHHHHHHHHTTS-TSSEEEEEEETTSSE
T ss_pred CEEEEEEECCeeEEEEEcCCCCCHHHHHHHHHHHhCCC-CccEEEEeeCCCCCE
Confidence 35677887777555 89999999999999999999987 667899999988744
No 22
>PF11470 TUG-UBL1: GLUT4 regulating protein TUG; InterPro: IPR021569 TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly. TUG releases the GLUT4 containing vesicles to the cellular exocytic machinery in response to insulin stimulation which allows translocation to the plasma membrane []. TUG has an N-terminal ubiquitin-like domain (UBL1) which in similar proteins appears to participate in protein-protein interactions []. The region does have a area of negative electrostatic potential and increased backbone motility which leads to suggestions of a potential protein-protein interaction site []. ; PDB: 2AL3_A.
Probab=90.89 E-value=0.3 Score=27.60 Aligned_cols=49 Identities=18% Similarity=0.313 Sum_probs=31.5
Q ss_pred cCC-eEEEEEcccCchhhhHHHHhcccCceeeeeeeEEEecCCCCeecccCCCeec
Q psy11813 12 MDA-ELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYADSRGDLTWIKLYKKVR 66 (70)
Q Consensus 12 LD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y~d~~~~~~WLd~~k~i~ 66 (70)
-++ ...+.+.+.++=.++++++|++.++... -++|.|.++. ||++-|++
T Consensus 4 ~~~rr~~vkvtp~~~l~~VL~eac~k~~l~~~-~~~L~h~~k~-----ldlslp~R 53 (65)
T PF11470_consen 4 YNFRRFKVKVTPNTTLNQVLEEACKKFGLDPS-SYDLKHNNKP-----LDLSLPFR 53 (65)
T ss_dssp TTS-EEEE---TTSBHHHHHHHHHHHTT--GG-G-EEEETTEE-----ESSS-BHH
T ss_pred cCCcEEEEEECCCCCHHHHHHHHHHHcCCCcc-ceEEEECCEE-----ecccccee
Confidence 445 6779999999999999999999998655 6688875321 56665553
No 23
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a 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 required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid 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
Probab=90.08 E-value=1.4 Score=26.25 Aligned_cols=49 Identities=18% Similarity=0.374 Sum_probs=40.0
Q ss_pred ecCC-eEEEEEcccCchhhhHHHHhcccCcee--eeeeeEEEecCCCCeecc
Q psy11813 11 TMDA-ELEFAIQHTTTGKQLFDQTVKTIGLRE--VWFFGLQYADSRGDLTWI 59 (70)
Q Consensus 11 lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E--~dYFGL~y~d~~~~~~WL 59 (70)
-..| .+.|.+.+...=.+|...|.+++++.. ..-|.|.|.|.++.+.=|
T Consensus 7 ~~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~~~~~~L~YlDDEgD~Vll 58 (86)
T cd06409 7 DPKGRVHRFRLRPSESLEELRTLISQRLGDDDFETHLYALSYVDDEGDIVLI 58 (86)
T ss_pred CCCCCEEEEEecCCCCHHHHHHHHHHHhCCccccCCcccEEEEcCCCCEEEE
Confidence 3346 577999998888999999999999865 478999999988876543
No 24
>cd01768 RA RA (Ras-associating) ubiquitin domain. The RA (Ras-associating) domain is structurally similar to ubiquitin and is present in one or two copies in a number of signalling molecules that bind and regulate a small GTPase called Ras or the Ras-related GTPases, Ral and Rap. RA-containing proteins include RalGDS, AF6, RIN1, RASSF1, SNX27, CYR1, STE50, and phospholipase C epsilon.
Probab=90.07 E-value=1.6 Score=24.82 Aligned_cols=47 Identities=21% Similarity=0.267 Sum_probs=38.6
Q ss_pred EEEEecC---Ce-EEEEEcccCchhhhHHHHhcccCce-eeeeeeEEEecCC
Q psy11813 7 VRVTTMD---AE-LEFAIQHTTTGKQLFDQTVKTIGLR-EVWFFGLQYADSR 53 (70)
Q Consensus 7 ~~V~lLD---~~-~~~~v~~~~~G~~L~d~Vc~~L~L~-E~dYFGL~y~d~~ 53 (70)
++|..-| ++ ..+.|++.++.+++...+.+..++. ....|.|.-.-.+
T Consensus 2 ikV~~~~~~~~~~kti~V~~~~t~~~Vi~~~l~k~~l~~~~~~y~L~ev~~~ 53 (87)
T cd01768 2 LRVYPEDPSGGTYKTLRVSKDTTAQDVIQQLLKKFGLDDDPEDYALVEVLGD 53 (87)
T ss_pred EEEeCCcCCCccEEEEEECCCCCHHHHHHHHHHHhCCcCCcccEEEEEEECC
Confidence 4667666 54 5699999999999999999999998 6678999875444
No 25
>PF00789 UBX: UBX domain; InterPro: IPR001012 The UBX domain is found in ubiquitin-regulatory proteins, which are members of the ubiquitination pathway, as well as a number of other proteins including FAF-1 (FAS-associated factor 1), the human Rep-8 reproduction protein and several hypothetical proteins from yeast. The function of the UBX domain is not known although the fragment of avian FAF-1 containing the UBX domain causes apoptosis of transfected cells.; GO: 0005515 protein binding; PDB: 3QX1_A 1H8C_A 3QCA_B 3QQ8_B 3QC8_B 3R3M_A 3QWZ_B 1S3S_H 1JRU_A 1I42_A ....
Probab=89.95 E-value=1.3 Score=25.03 Aligned_cols=47 Identities=19% Similarity=0.166 Sum_probs=39.2
Q ss_pred ceEEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCceeeeeeeEEE
Q psy11813 3 GLMNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQY 49 (70)
Q Consensus 3 ~~~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y 49 (70)
....++|.+.|| .+.-...+.++-++|++-|-.++...+...|-|.-
T Consensus 5 ~~~~I~vRlpdG~~l~~~F~~~~tl~~l~~~v~~~~~~~~~~~f~L~~ 52 (82)
T PF00789_consen 5 DVVRIQVRLPDGSRLQRRFPKSDTLQDLYDFVESQLFSPEESDFELIT 52 (82)
T ss_dssp SEEEEEEEETTSTEEEEEEETTSBHHHHHHHHHHHHHCTTTSSEEEEE
T ss_pred CEEEEEEECCCCCEEEEEECCcchHHHHHHHHHHhcCCCCCccEEEEe
Confidence 457899999999 78888889999999999999988877665577753
No 26
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=89.94 E-value=0.98 Score=23.61 Aligned_cols=44 Identities=18% Similarity=0.299 Sum_probs=34.8
Q ss_pred EEEEEEecCCeEEEEEcccCchhhhHHHHhcccCceeeeeeeEEE
Q psy11813 5 MNVRVTTMDAELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQY 49 (70)
Q Consensus 5 ~~~~V~lLD~~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y 49 (70)
|.+.|...++...+.+++.++..+|-.++.+..++.. +..-|.|
T Consensus 1 ~~i~vk~~~~~~~~~v~~~~tv~~lk~~i~~~~~~~~-~~~~L~~ 44 (64)
T smart00213 1 IELTVKTLDGTITLEVKPSDTVSELKEKIAELTGIPV-EQQRLIY 44 (64)
T ss_pred CEEEEEECCceEEEEECCCCcHHHHHHHHHHHHCCCH-HHEEEEE
Confidence 4678888886677999999999999999999998743 3344444
No 27
>PF02196 RBD: Raf-like Ras-binding domain; InterPro: IPR003116 This is the Ras-binding domain found in proteins related to Ras. It is found in association with the PE-bind and pkinase domains.; GO: 0005057 receptor signaling protein activity, 0007165 signal transduction; PDB: 1RFA_A 1C1Y_B 3KUD_B 1GUA_B 3KUC_B 2L05_A 3NY5_D 1RRB_A 1WFY_A 1WXM_A.
Probab=89.39 E-value=1.7 Score=24.66 Aligned_cols=38 Identities=16% Similarity=0.185 Sum_probs=30.4
Q ss_pred EEEEEecCCe-EEEEEcccCchhhhHHHHhcccCceeee
Q psy11813 6 NVRVTTMDAE-LEFAIQHTTTGKQLFDQTVKTIGLREVW 43 (70)
Q Consensus 6 ~~~V~lLD~~-~~~~v~~~~~G~~L~d~Vc~~L~L~E~d 43 (70)
.|+|.|-|++ ..+.+.+.-+-++.+..+|+.-+|.-.+
T Consensus 2 ~~~v~LP~~q~t~V~vrpg~ti~d~L~~~~~kr~L~~~~ 40 (71)
T PF02196_consen 2 TCRVHLPNGQRTVVQVRPGMTIRDALSKACKKRGLNPEC 40 (71)
T ss_dssp EEEEEETTTEEEEEEE-TTSBHHHHHHHHHHTTT--CCC
T ss_pred eEEEECCCCCEEEEEEcCCCCHHHHHHHHHHHcCCCHHH
Confidence 5899999994 5699999999999999999999875443
No 28
>smart00455 RBD Raf-like Ras-binding domain.
Probab=88.59 E-value=2 Score=24.36 Aligned_cols=44 Identities=14% Similarity=0.136 Sum_probs=35.5
Q ss_pred EEEEEecCC-eEEEEEcccCchhhhHHHHhcccCceeeeeeeEEEe
Q psy11813 6 NVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYA 50 (70)
Q Consensus 6 ~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y~ 50 (70)
.|+|.+-|+ ...+.+.+.-+-+++++.+|+.-|| +.+.-.+...
T Consensus 1 ~~~v~LP~~~~~~V~vrpg~tl~e~L~~~~~kr~l-~~~~~~v~~~ 45 (70)
T smart00455 1 TCKVHLPDNQRTVVKVRPGKTVRDALAKALKKRGL-NPECCVVRLR 45 (70)
T ss_pred CeEEECCCCCEEEEEECCCCCHHHHHHHHHHHcCC-CHHHEEEEEc
Confidence 378999999 6779999999999999999999998 3444445443
No 29
>cd01760 RBD Ubiquitin-like domain of RBD-like S/T kinases. The ras-binding domain (RBD) of the serine/threonine kinase raf is structurally quite similar to the beta-grasp fold of ubiquitin. A raf-like RBD is also present in RGS12 and other members of a family of GTPase activating proteins and TIAM1, a guanine nucleotide exchange protein.
Probab=88.17 E-value=1 Score=25.87 Aligned_cols=44 Identities=11% Similarity=0.113 Sum_probs=35.3
Q ss_pred EEEEEecCC-eEEEEEcccCchhhhHHHHhcccCceeeeeeeEEEe
Q psy11813 6 NVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYA 50 (70)
Q Consensus 6 ~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y~ 50 (70)
.|+|.|-|| ...+.+.+..+-+++++.+|+.-+|.-..| .|...
T Consensus 1 ~~~V~LPng~~t~V~vrpg~ti~d~L~~~c~kr~l~~~~~-~v~~~ 45 (72)
T cd01760 1 LCRVYLPNGQRTVVPVRPGMSVRDVLAKACKKRGLNPECC-DVFLL 45 (72)
T ss_pred CEEEECcCCCeEEEEECCCCCHHHHHHHHHHHcCCCHHHE-EEEEe
Confidence 489999999 566999999999999999999999864433 34443
No 30
>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=88.13 E-value=1.6 Score=23.66 Aligned_cols=44 Identities=23% Similarity=0.393 Sum_probs=35.1
Q ss_pred EEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCceeeeeeeEEE
Q psy11813 5 MNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQY 49 (70)
Q Consensus 5 ~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y 49 (70)
|.+.|..++| +..+.+++..+-.+|-+++.+..++. .+..-|.|
T Consensus 1 i~i~vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gi~-~~~q~L~~ 45 (72)
T cd01809 1 IEIKVKTLDSQTHTFTVEEEITVLDLKEKIAEEVGIP-VEQQRLIY 45 (72)
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcC-HHHeEEEE
Confidence 5678999998 78899999999999999999998863 33334444
No 31
>smart00314 RA Ras association (RalGDS/AF-6) domain. RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Kalhammer et al. have shown that not all RA domains bind RasGTP. Predicted structure similar to that determined, and that of the RasGTP-binding domain of Raf kinase. Predicted RA domains in PLC210 and nore1 found to bind RasGTP. Included outliers (Grb7, Grb14, adenylyl cyclases etc.)
Probab=87.37 E-value=3.8 Score=23.40 Aligned_cols=47 Identities=17% Similarity=0.163 Sum_probs=38.2
Q ss_pred EEEEEEecC---Ce-EEEEEcccCchhhhHHHHhcccCcee-eeeeeEEEec
Q psy11813 5 MNVRVTTMD---AE-LEFAIQHTTTGKQLFDQTVKTIGLRE-VWFFGLQYAD 51 (70)
Q Consensus 5 ~~~~V~lLD---~~-~~~~v~~~~~G~~L~d~Vc~~L~L~E-~dYFGL~y~d 51 (70)
..++|..-| ++ ..+.|.+.++.++++..+.+..++.. ...|.|.-.-
T Consensus 3 ~~lrV~~~~~~~~~~kti~v~~~tTa~~Vi~~~l~k~~l~~~~~~y~L~e~~ 54 (90)
T smart00314 3 FVLRVYVDDLPGGTYKTLRVSSRTTARDVIQQLLEKFHLTDDPEEYVLVEVL 54 (90)
T ss_pred eEEEEecccCCCCcEEEEEECCCCCHHHHHHHHHHHhCCCCCcccEEEEEEe
Confidence 357777766 64 56999999999999999999999976 5677877654
No 32
>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=85.99 E-value=3.7 Score=24.24 Aligned_cols=47 Identities=13% Similarity=0.147 Sum_probs=38.6
Q ss_pred EEEEEEecCCeEEEEEcccCchhhhHHHHhcccCceeeeeeeEEEecCC
Q psy11813 5 MNVRVTTMDAELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYADSR 53 (70)
Q Consensus 5 ~~~~V~lLD~~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y~d~~ 53 (70)
..++|++=+ ++-+.+++...=++|.++|+++|.|. .+--=|+|.+..
T Consensus 3 ~vvKV~f~~-tIaIrvp~~~~y~~L~~ki~~kLkl~-~e~i~LsYkde~ 49 (80)
T cd06406 3 YVVKVHFKY-TVAIQVARGLSYATLLQKISSKLELP-AEHITLSYKSEA 49 (80)
T ss_pred eEEEEEEEE-EEEEEcCCCCCHHHHHHHHHHHhCCC-chhcEEEeccCC
Confidence 567788776 78899999999999999999999995 333678897654
No 33
>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=85.78 E-value=2.8 Score=23.75 Aligned_cols=35 Identities=20% Similarity=0.386 Sum_probs=31.7
Q ss_pred EEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCc
Q psy11813 5 MNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGL 39 (70)
Q Consensus 5 ~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L 39 (70)
|.+.|..+.| ++.+.+++.++-.+|-+++.+..++
T Consensus 3 ~~i~Vk~~~G~~~~~~v~~~~TV~~lK~~I~~~~~i 38 (80)
T cd01792 3 WDLKVKMLGGNEFLVSLRDSMTVSELKQQIAQKIGV 38 (80)
T ss_pred eEEEEEeCCCCEEEEEcCCCCcHHHHHHHHHHHhCC
Confidence 7888999998 7889999999999999999998886
No 34
>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=85.48 E-value=2.6 Score=23.40 Aligned_cols=38 Identities=13% Similarity=0.183 Sum_probs=33.0
Q ss_pred EEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCceee
Q psy11813 5 MNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREV 42 (70)
Q Consensus 5 ~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~ 42 (70)
|.+.|..++| +..+.+++..+-.+|-+++++.-|+...
T Consensus 1 m~i~vk~~~G~~~~l~v~~~~tV~~lK~~i~~~~gi~~~ 39 (74)
T cd01807 1 MFLTVKLLQGRECSLQVSEKESVSTLKKLVSEHLNVPEE 39 (74)
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHH
Confidence 5678999999 7789999999999999999999987543
No 35
>cd01787 GRB7_RA RA (RAS-associated like) domain of Grb7. Grb7_RA The RA (RAS-associated like) domain of Grb7. Grb7 is an adaptor molecule that mediates signal transduction from multiple cell surface receptors to various downstream signaling pathways. Grb7 and its related family members Grb10 and Grb14 share a conserved domain architecture that includes an amino-terminal proline-rich region, a central segment termed the GM region (for Grb and Mig) which includes the RA, PIR, and PH domains, and a carboxyl-terminal SH2 domain. Grb7/10/14 family proteins are phosphorylated on serine/threonine as well as tyrosine residues and are mainly localized to the cytoplasm.
Probab=84.34 E-value=3.8 Score=24.47 Aligned_cols=45 Identities=13% Similarity=0.113 Sum_probs=38.5
Q ss_pred eEEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCceeeeeeeEE
Q psy11813 4 LMNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQ 48 (70)
Q Consensus 4 ~~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~ 48 (70)
...|+|.+.|| +-.+.|+...+.+++.+..++.-.+.......|-
T Consensus 2 k~vvkv~~~Dg~sK~l~V~~~~Ta~dV~~~L~~K~h~~~~~~W~Lv 47 (85)
T cd01787 2 KQVVKVYSEDGASKSLEVDERMTARDVCQLLVDKNHCQDDSSWTLV 47 (85)
T ss_pred ceEEEEEecCCCeeEEEEcCCCcHHHHHHHHHHHhCCCCCCCeEEE
Confidence 45799999999 6779999999999999999999888776666664
No 36
>KOG3784|consensus
Probab=84.17 E-value=2.1 Score=32.12 Aligned_cols=47 Identities=15% Similarity=0.346 Sum_probs=38.4
Q ss_pred EEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCcee--eeeeeEEEec
Q psy11813 5 MNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLRE--VWFFGLQYAD 51 (70)
Q Consensus 5 ~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E--~dYFGL~y~d 51 (70)
....|-+.+| .+++++-.+.+...+|..||..|++.. .-||||.-..
T Consensus 108 v~l~v~lpng~~i~i~~~~s~tt~~vl~~v~~kl~l~~e~i~~f~lFlvr 157 (407)
T KOG3784|consen 108 VELDVFLPNGEKITINCLVSDTASLVLKSVCRKLGLPDELIGYFGLFLVR 157 (407)
T ss_pred eEEEEEccCCceEEEEEEecccHHHHHHHHHhhcCCchHhhhheeeeEEe
Confidence 4556667788 688999999999999999999999962 2499998753
No 37
>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=83.10 E-value=4 Score=22.47 Aligned_cols=35 Identities=14% Similarity=0.250 Sum_probs=31.2
Q ss_pred EEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCc
Q psy11813 5 MNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGL 39 (70)
Q Consensus 5 ~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L 39 (70)
|.+.|..++| ++.+.+++..+-.+|-+++++..++
T Consensus 1 m~i~vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~i 36 (77)
T cd01805 1 MKITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGC 36 (77)
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHhhCC
Confidence 5678888999 7889999999999999999998886
No 38
>KOG3531|consensus
Probab=82.63 E-value=0.05 Score=44.02 Aligned_cols=62 Identities=3% Similarity=-0.287 Sum_probs=49.0
Q ss_pred eEEEEEEecCCeEEEEEcccCchhhhHHHHhcccCceeeeeeeEEEec-CCCCeecccCCCee
Q psy11813 4 LMNVRVTTMDAELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYAD-SRGDLTWIKLYKKV 65 (70)
Q Consensus 4 ~~~~~V~lLD~~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y~d-~~~~~~WLd~~k~i 65 (70)
...+++..++....+-+++.+.|+.+|..+|..+++.|.+|||++|.- .-..+.|+|.+++-
T Consensus 177 ~~~l~~~~~~p~q~~~~~ki~~~h~~hig~tpaesdl~~le~ar~~~~yg~~~h~a~D~Eg~~ 239 (1036)
T KOG3531|consen 177 REHLAHTRYLPNQDELEKKIMEFHQKHIGQTPAESDFQLLEIARRLDMYGIRLHPAKDREGTK 239 (1036)
T ss_pred ceeeeeeecCchHHHHHHHHHHhhhhhhccCchhhhHHHHHHHHHHhhhccccchhhhcccch
Confidence 346777777763366678899999999999999999999999999832 23456799988763
No 39
>PTZ00044 ubiquitin; Provisional
Probab=82.21 E-value=4.2 Score=22.40 Aligned_cols=37 Identities=16% Similarity=0.229 Sum_probs=32.4
Q ss_pred EEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCcee
Q psy11813 5 MNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLRE 41 (70)
Q Consensus 5 ~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E 41 (70)
|.+.|..++| +..+.+++..+-.+|=.++.+..++..
T Consensus 1 m~i~vk~~~G~~~~l~v~~~~tv~~lK~~i~~~~gi~~ 38 (76)
T PTZ00044 1 MQILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDV 38 (76)
T ss_pred CEEEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCH
Confidence 4678999999 788999999999999999999999743
No 40
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=82.21 E-value=4.1 Score=22.17 Aligned_cols=36 Identities=14% Similarity=0.260 Sum_probs=31.8
Q ss_pred EEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCce
Q psy11813 5 MNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLR 40 (70)
Q Consensus 5 ~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~ 40 (70)
|.+.|..++| .+.+.+++..+-.+|-+++.+..++.
T Consensus 1 m~i~v~~~~g~~~~~~v~~~~tV~~lK~~i~~~~g~~ 37 (76)
T cd01803 1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIP 37 (76)
T ss_pred CEEEEEcCCCCEEEEEECCcCcHHHHHHHHHHHhCCC
Confidence 4678999998 78899999999999999999998874
No 41
>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=78.18 E-value=13 Score=22.73 Aligned_cols=62 Identities=18% Similarity=0.048 Sum_probs=45.8
Q ss_pred eEEEEEEecCCe-EEEEEcccCchhhhHHHHhcccCceeeeeeeEEEecCCCCeecccCCCee
Q psy11813 4 LMNVRVTTMDAE-LEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYADSRGDLTWIKLYKKV 65 (70)
Q Consensus 4 ~~~~~V~lLD~~-~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y~d~~~~~~WLd~~k~i 65 (70)
...++|--.|++ .++.+..+++-+++...+-+...|.+..-|-|...-.+-.+.-...+||+
T Consensus 2 ~y~IRIFr~D~Tf~Tls~~l~tTv~eli~~L~rK~~l~~~~ny~l~l~~~~l~RvL~p~ErPl 64 (97)
T cd01775 2 SYCIRVFRSDGTFTTLSCPLNTTVSELIPQLAKKFYLPSGGNYQLSLKKHDLSRVLRPTEKPL 64 (97)
T ss_pred ceEEEEEecCCcEEEEEcCCcCcHHHHHHHHHHhhcCCCCCCeEEEEEECCeeeecCCcCCcH
Confidence 456899999997 56999999999999999999999987665566555444444433345554
No 42
>PF13019 Telomere_Sde2: Telomere stability and silencing
Probab=76.93 E-value=9.7 Score=25.24 Aligned_cols=46 Identities=24% Similarity=0.272 Sum_probs=37.3
Q ss_pred EEEEEEecCC-----eEEEEEcccCchhhhHHHHhcccCceeeeeeeEEEe
Q psy11813 5 MNVRVTTMDA-----ELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYA 50 (70)
Q Consensus 5 ~~~~V~lLD~-----~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y~ 50 (70)
|++-|+.+|+ ++.+.++..++-.+|++.+...+...-..-+-|.+.
T Consensus 1 i~Vlvss~~g~~lp~tl~~~lp~~ttv~dL~~~l~~~~~~~~~~~~~L~~~ 51 (162)
T PF13019_consen 1 INVLVSSFDGLTLPPTLSLSLPSTTTVSDLKDRLSERLPIPSSSQLYLTTN 51 (162)
T ss_pred CeEEEecCCCCCCCCeEEeeCCCCCcHHHHHHHHHhhcCCCccceeEEEEe
Confidence 4678999998 466888999999999999999999876654555554
No 43
>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=76.22 E-value=10 Score=21.40 Aligned_cols=35 Identities=11% Similarity=0.283 Sum_probs=31.4
Q ss_pred EEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCc
Q psy11813 5 MNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGL 39 (70)
Q Consensus 5 ~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L 39 (70)
|.+.|..+.| ..++++++.++-.+|-+++.+..++
T Consensus 2 m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~~~ 37 (78)
T cd01804 2 MNLNIHSTTGTRFDLSVPPDETVEGLKKRISQRLKV 37 (78)
T ss_pred eEEEEEECCCCEEEEEECCcCHHHHHHHHHHHHhCC
Confidence 6788999988 7889999999999999999988875
No 44
>TIGR01961 NuoC_fam NADH (or F420H2) dehydrogenase, subunit C. This model describes the C subunit of the NADH dehydrogenase complex I in bacteria, as well as many instances of the corresponding mitochondrial subunit (NADH dehydrogenase subunit 9) and of the F420H2 dehydrogenase in Methanosarcina. Complex I contains subunits designated A-N. This C subunit often occurs as a fusion protein with the D subunit. This model excludes the NAD(P)H and plastoquinone-dependent form of chloroplasts and
Probab=70.01 E-value=2.6 Score=25.70 Aligned_cols=33 Identities=9% Similarity=0.046 Sum_probs=26.3
Q ss_pred HHHHhcccCceee---eeeeEEEecCCCCeecccCC
Q psy11813 30 FDQTVKTIGLREV---WFFGLQYADSRGDLTWIKLY 62 (70)
Q Consensus 30 ~d~Vc~~L~L~E~---dYFGL~y~d~~~~~~WLd~~ 62 (70)
+..++...+..|+ |.||+.|..+.+.+.|+.++
T Consensus 71 is~i~p~A~~~EREi~DmfGi~f~Ghpd~rr~ll~~ 106 (121)
T TIGR01961 71 LTSVFPTANWYERETYDMYGIVFDGHPDLRRILMPD 106 (121)
T ss_pred hHHhhhcccHHHHHHHhhcCcEeCCCCCCccccCCC
Confidence 4556666777776 69999999998889999874
No 45
>cd01817 RGS12_RBD Ubiquitin domain of RGS12 and RGS14. RGS12 (regulator of G signalling 12), and RGS14, are members of a family of GTPase-activating proteins (GAP's) specific for the G-alpha subunit, which act as key inhibitors of G-protein-mediated cell responses in eukaryotes. Their domain architecture includes tandem RBD domains as well as PDZ , PTB, and RGS, and GoLoco domains.
Probab=69.48 E-value=11 Score=21.82 Aligned_cols=35 Identities=14% Similarity=0.149 Sum_probs=30.3
Q ss_pred EEEEEecCCe-EEEEEcccCchhhhHHHHhcccCce
Q psy11813 6 NVRVTTMDAE-LEFAIQHTTTGKQLFDQTVKTIGLR 40 (70)
Q Consensus 6 ~~~V~lLD~~-~~~~v~~~~~G~~L~d~Vc~~L~L~ 40 (70)
.|+|.|-|++ -.+.+.+.-+=++++...|+.-+|.
T Consensus 1 ~crV~LPdg~~T~V~vrpG~ti~d~L~kllekRgl~ 36 (73)
T cd01817 1 LCRVILPDGSTTVVPTRPGESIRDLLSGLCEKRGIN 36 (73)
T ss_pred CcEEECCCCCeEEEEecCCCCHHHHHHHHHHHcCCC
Confidence 3899999994 5589999889999999999998875
No 46
>cd01818 TIAM1_RBD Ubiquitin domain of Tiam1 guanine nucleotide exchange factor. Tiam1 (T lymphoma invasion and metastasis 1) a guanine nucleotide exchange factor that activates Rac, is an important regulator of Rho GTPase functions in tumor cells including regulation of cell shape and invasiveness in epithelial cells and fibroblasts. TIAM1 has an RBD (Ras-binding domain) similar to that of Raf kinase as well as PH (pleckstrin homology), PDZ, and RhoGEF domains.
Probab=67.52 E-value=9.5 Score=22.44 Aligned_cols=43 Identities=12% Similarity=0.167 Sum_probs=34.5
Q ss_pred EEEecCC-eEEEEEcccCchhhhHHHHhcccCceeee-eeeEEEe
Q psy11813 8 RVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREVW-FFGLQYA 50 (70)
Q Consensus 8 ~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~d-YFGL~y~ 50 (70)
.|.+-|| ...+.|.+.-+-.++++..|+.=++.-.+ |.-|.+.
T Consensus 3 ~V~lPn~~~~~v~vrp~~tv~dvLe~aCk~~~ldp~eh~Lrlk~~ 47 (77)
T cd01818 3 WVCLPDNQPVLTYLRPGMSVEDFLESACKRKQLDPMEHYLRLKFL 47 (77)
T ss_pred EEECCCCceEEEEECCCCCHHHHHHHHHHhcCCChhHheeEEEEE
Confidence 4778888 57899999999999999999999985554 4445554
No 47
>PRK12494 NADH dehydrogenase subunit J; Provisional
Probab=67.15 E-value=2.6 Score=27.82 Aligned_cols=33 Identities=9% Similarity=-0.001 Sum_probs=26.4
Q ss_pred HHHHhcccCceee---eeeeEEEecCCCCeecccCC
Q psy11813 30 FDQTVKTIGLREV---WFFGLQYADSRGDLTWIKLY 62 (70)
Q Consensus 30 ~d~Vc~~L~L~E~---dYFGL~y~d~~~~~~WLd~~ 62 (70)
+..++...+..|+ |.||+.|.++.+.+.||.++
T Consensus 114 It~i~p~A~w~EREi~DmfGI~FeGHPDlRriLlpe 149 (172)
T PRK12494 114 VYWIWKGADWQERETYDMYGINFEGHPNLKRILMPE 149 (172)
T ss_pred hhHhhhcCChHHHHHHHhcCceeCCCCCCccccCCC
Confidence 4566667777776 69999999998999998863
No 48
>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=65.79 E-value=22 Score=21.31 Aligned_cols=38 Identities=13% Similarity=0.155 Sum_probs=33.3
Q ss_pred ceEEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCce
Q psy11813 3 GLMNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLR 40 (70)
Q Consensus 3 ~~~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~ 40 (70)
..|.+.|..+.| ++.+++++.++=.+|-+++.+.-++.
T Consensus 26 ~~M~I~Vk~l~G~~~~leV~~~~TV~~lK~kI~~~~gip 64 (103)
T cd01802 26 DTMELFIETLTGTCFELRVSPFETVISVKAKIQRLEGIP 64 (103)
T ss_pred CCEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHHhCCC
Confidence 358999999999 78899999999999999999887764
No 49
>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=65.00 E-value=20 Score=19.17 Aligned_cols=36 Identities=19% Similarity=0.216 Sum_probs=29.3
Q ss_pred EEEEEEecCCeEEEEEcccCchhhhHHHHhcccCce
Q psy11813 5 MNVRVTTMDAELEFAIQHTTTGKQLFDQTVKTIGLR 40 (70)
Q Consensus 5 ~~~~V~lLD~~~~~~v~~~~~G~~L~d~Vc~~L~L~ 40 (70)
+.+.|.......++.+++.++-.+|-+++.+.-++.
T Consensus 1 i~i~vk~~g~~~~i~v~~~~tv~~lK~~i~~~~gi~ 36 (71)
T cd01812 1 IRVRVKHGGESHDLSISSQATFGDLKKMLAPVTGVE 36 (71)
T ss_pred CEEEEEECCEEEEEEECCCCcHHHHHHHHHHhhCCC
Confidence 456777762277899999999999999999988864
No 50
>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells. PB1 domain is a modular domain mediating specific protein-protein interaction which play roles 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,
Probab=61.63 E-value=32 Score=20.45 Aligned_cols=53 Identities=17% Similarity=0.188 Sum_probs=40.7
Q ss_pred EEEEecCCeEEEEEcccCchhhhHHHHhcccCceeeeeeeEEEecCCCCeecc
Q psy11813 7 VRVTTMDAELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYADSRGDLTWI 59 (70)
Q Consensus 7 ~~V~lLD~~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y~d~~~~~~WL 59 (70)
+++..=.+.+-+.+++..+=.+|-++|-+--.+.+..-|.+.|.|.+|.++=+
T Consensus 3 ~K~~y~gdi~it~~d~~~s~e~L~~~v~~~c~~~~~q~ft~kw~DEEGDp~ti 55 (83)
T cd06404 3 VKAAYNGDIMITSIDPSISLEELCNEVRDMCRFHNDQPFTLKWIDEEGDPCTI 55 (83)
T ss_pred EEEEecCcEEEEEcCCCcCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCceee
Confidence 44444444566888888888888888888888888889999999998866543
No 51
>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=60.55 E-value=19 Score=19.46 Aligned_cols=35 Identities=23% Similarity=0.171 Sum_probs=30.1
Q ss_pred EEEecCC-eEEEEEcccCchhhhHHHHhcccCceee
Q psy11813 8 RVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREV 42 (70)
Q Consensus 8 ~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~ 42 (70)
.|..++| ++.+.+++..+-.++-+++++..|+...
T Consensus 2 ~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~ 37 (70)
T cd01798 2 YVRTNTGHTFPVEVDPDTDIKQLKEVVAKRQGVPPD 37 (70)
T ss_pred EEEcCCCCEEEEEECCCChHHHHHHHHHHHHCCCHH
Confidence 4778888 7889999999999999999999987543
No 52
>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=59.34 E-value=13 Score=17.64 Aligned_cols=40 Identities=25% Similarity=0.202 Sum_probs=29.2
Q ss_pred EEecCC-eEEEEEcccCchhhhHHHHhcccCceeeeeeeEEE
Q psy11813 9 VTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQY 49 (70)
Q Consensus 9 V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y 49 (70)
|.+-++ ...+.+.+.++-.++.+.+++..+. ..+.|-|.+
T Consensus 2 v~~~~~~~~~~~~~~~~tv~~l~~~i~~~~~~-~~~~~~l~~ 42 (69)
T cd00196 2 VKLNDGKTVELLVPSGTTVADLKEKLAKKLGL-PPEQQRLLV 42 (69)
T ss_pred eEecCCCEEEEEcCCCCcHHHHHHHHHHHHCc-ChHHeEEEE
Confidence 444466 5678888999999999999999883 334455555
No 53
>cd00419 Ferrochelatase_C Ferrochelatase, C-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is ubiquitous in nature and widely distributed in bacteria and eukaryotes. Recently, some archaeal members have been identified. The oligomeric state of these enzymes varies depending on the presence of a dimerization motif at the C-terminus.
Probab=57.11 E-value=13 Score=23.22 Aligned_cols=34 Identities=18% Similarity=0.265 Sum_probs=25.6
Q ss_pred hhHHHHhcccCceeeeeeeEEEecCCCCeecccCC
Q psy11813 28 QLFDQTVKTIGLREVWFFGLQYADSRGDLTWIKLY 62 (70)
Q Consensus 28 ~L~d~Vc~~L~L~E~dYFGL~y~d~~~~~~WLd~~ 62 (70)
+..++|.+.+++.... +.+.|++..+.-.||.|+
T Consensus 45 ~~~~~v~~~l~~~~~~-~~~~fqS~~g~~~Wl~P~ 78 (135)
T cd00419 45 ETARLVAERLGLPFDE-YELAYQSRFGPGEWLEPS 78 (135)
T ss_pred HHHHHHHHHhCCCCCC-EEEEecCCCCCCCCCCCC
Confidence 3456788888865544 469999888888899875
No 54
>cd01776 Rin1_RA Ubiquitin domain of RIN1 RAS effector. Rin1_RA RIN1 is a RAS effector that binds with specificity and high affinity to activated RAS via its carboxy-terminal RA (RAS-associated) domain. RIN1 competes directly with RAF1 for RAS binding and is thought to divert signaling away from RAF and the MAPK pathway while also shunting RAS signals through alternate pathways. In addition, Rin1 and Rin2 are Rab5-binding proteins, binding preferentially to the GTP-bound form, that enhance the GDP-GTP exchange reaction on Rab5 that regulate the docking and fusion processes of endocytic vesicles. In addition to the RA domain, RIN1 and RIN2 have an SH2 (Src homology 2) domain, a proline-rich SH3 domain, and a Vps9 domain.
Probab=56.23 E-value=42 Score=20.13 Aligned_cols=53 Identities=8% Similarity=0.071 Sum_probs=40.8
Q ss_pred EEEEe--cCC--e-EEEEEcccCchhhhHHHHhcccCceeeeeeeEEEecCCCCeeccc
Q psy11813 7 VRVTT--MDA--E-LEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYADSRGDLTWIK 60 (70)
Q Consensus 7 ~~V~l--LD~--~-~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y~d~~~~~~WLd 60 (70)
.+|.+ +|+ + -++-|.+.++-++|=.++.+...+.+.+-|||-..- ++..+=|.
T Consensus 2 l~Va~q~~~sgct~KTL~V~P~~tt~~vc~lcA~Kf~V~qPe~y~LFl~v-dg~~~qLa 59 (87)
T cd01776 2 LRVAFQDVNSGCTGKTLLVRPYITTEDVCQLCAEKFKVTQPEEYSLFLFV-EETWQQLA 59 (87)
T ss_pred eeEEeecCCCCceeeeeecCCCCcHHHHHHHHHHHhccCChhheeEEEEE-CCcEEEcC
Confidence 35666 775 3 358899999999999999999999999999998753 33344343
No 55
>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=56.05 E-value=27 Score=18.10 Aligned_cols=40 Identities=20% Similarity=0.224 Sum_probs=30.1
Q ss_pred EEecCC-eEEEEEcccCchhhhHHHHhcccCceeeeeeeEEE
Q psy11813 9 VTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQY 49 (70)
Q Consensus 9 V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y 49 (70)
|...++ .+.+.+++.++..+|-+++.+..++... ..-|.|
T Consensus 2 v~~~~~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~-~~~l~~ 42 (69)
T cd01769 2 VKTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPE-QQRLIY 42 (69)
T ss_pred eEccCCCEEEEEECCCChHHHHHHHHHHHHCcChH-HEEEEE
Confidence 556677 7789999999999999999998886432 234444
No 56
>PF14847 Ras_bdg_2: Ras-binding domain of Byr2; PDB: 1I35_A 1K8R_B.
Probab=55.44 E-value=28 Score=21.32 Aligned_cols=36 Identities=17% Similarity=0.264 Sum_probs=27.0
Q ss_pred EEEEEecCCe-EEEEEcccCchhhhHHHHhcccCcee
Q psy11813 6 NVRVTTMDAE-LEFAIQHTTTGKQLFDQTVKTIGLRE 41 (70)
Q Consensus 6 ~~~V~lLD~~-~~~~v~~~~~G~~L~d~Vc~~L~L~E 41 (70)
.++|..-||+ -.+.|..=..|+++...|.+.+++.+
T Consensus 2 vi~~I~~dG~tk~VNV~~c~~a~eI~~rvLKKfg~~~ 38 (105)
T PF14847_consen 2 VIRFILEDGSTKTVNVSGCFNAQEIKRRVLKKFGLPE 38 (105)
T ss_dssp EEEEEETTTEEEEEE--S--HHHHHHHHHHHHHTSS-
T ss_pred EEEEECCCCcEEEEEECCCCCHHHHHHHHHHHcCCcc
Confidence 3678888884 56999988899999999999999988
No 57
>PRK07735 NADH dehydrogenase subunit C; Validated
Probab=55.23 E-value=4.4 Score=30.66 Aligned_cols=32 Identities=9% Similarity=-0.040 Sum_probs=24.9
Q ss_pred HHHhcccCceee---eeeeEEEecCCCCeecccCC
Q psy11813 31 DQTVKTIGLREV---WFFGLQYADSRGDLTWIKLY 62 (70)
Q Consensus 31 d~Vc~~L~L~E~---dYFGL~y~d~~~~~~WLd~~ 62 (70)
..|+...+..|+ |.||+.|.++.+.++||.++
T Consensus 378 t~I~P~AnW~EREa~DMFGI~FeGHPDLRRILLpd 412 (430)
T PRK07735 378 TPLWKGANWPEREAYDLLGIVFKGHPNLSRILLPD 412 (430)
T ss_pred HHhhccCChHHHHHHHHhCcccCCCCCCccCCCCC
Confidence 345555666666 69999999999999998764
No 58
>KOG0005|consensus
Probab=54.58 E-value=29 Score=19.75 Aligned_cols=46 Identities=22% Similarity=0.351 Sum_probs=35.3
Q ss_pred EEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCceee----eeeeEEEe
Q psy11813 5 MNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREV----WFFGLQYA 50 (70)
Q Consensus 5 ~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~----dYFGL~y~ 50 (70)
|.++|..|-+ ++++++++..+-..+=+.|-+.-|+.-. -|=|-|-.
T Consensus 1 m~iKvktLt~KeIeidIep~DkverIKErvEEkeGIPp~qqrli~~gkqm~ 51 (70)
T KOG0005|consen 1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYAGKQMN 51 (70)
T ss_pred CeeeEeeeccceEEEeeCcchHHHHHHHHhhhhcCCCchhhhhhhcccccc
Confidence 4578999999 8999999999888888888888887532 25555543
No 59
>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=54.48 E-value=35 Score=19.07 Aligned_cols=35 Identities=17% Similarity=-0.020 Sum_probs=27.7
Q ss_pred EEEEEecCCeEEEEEcccCchhhhHHHHhcccCce
Q psy11813 6 NVRVTTMDAELEFAIQHTTTGKQLFDQTVKTIGLR 40 (70)
Q Consensus 6 ~~~V~lLD~~~~~~v~~~~~G~~L~d~Vc~~L~L~ 40 (70)
.+.|..-..++++++++.++..+|-+++++..++.
T Consensus 2 ~i~vk~~g~~~~v~v~~~~Tv~~lK~~i~~~tgvp 36 (74)
T cd01813 2 PVIVKWGGQEYSVTTLSEDTVLDLKQFIKTLTGVL 36 (74)
T ss_pred EEEEEECCEEEEEEECCCCCHHHHHHHHHHHHCCC
Confidence 34455433378899999999999999999999963
No 60
>PRK06074 NADH dehydrogenase subunit C; Provisional
Probab=53.47 E-value=6.4 Score=26.26 Aligned_cols=33 Identities=9% Similarity=0.061 Sum_probs=25.3
Q ss_pred HHHhcccCceee---eeeeEEEecCCCCeecccCCC
Q psy11813 31 DQTVKTIGLREV---WFFGLQYADSRGDLTWIKLYK 63 (70)
Q Consensus 31 d~Vc~~L~L~E~---dYFGL~y~d~~~~~~WLd~~k 63 (70)
..++...+-.|+ |.||+.|..+.+.++||.++.
T Consensus 102 t~i~p~A~w~EREi~DmfGI~f~GhPdlrrlllpe~ 137 (189)
T PRK06074 102 VDIWPSANWYEREAYDLYGIVFEGHPDLRRILTDYG 137 (189)
T ss_pred HHhhhccChHHHHHHHhhCceeCCCCCCccccCCCC
Confidence 445555666666 699999999999999988643
No 61
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=51.85 E-value=42 Score=18.77 Aligned_cols=45 Identities=11% Similarity=0.074 Sum_probs=32.5
Q ss_pred ceEEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCceeeeeeeEE
Q psy11813 3 GLMNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQ 48 (70)
Q Consensus 3 ~~~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~ 48 (70)
....++|++-|| .+.-......+=++|++-|....+. +..-|-|.
T Consensus 3 ~~~~I~iRlPdG~ri~~~F~~~~tl~~v~~~v~~~~~~-~~~~f~L~ 48 (80)
T smart00166 3 DQCRLQIRLPDGSRLVRRFPSSDTLRTVYEFVSAALTD-GNDPFTLN 48 (80)
T ss_pred CeEEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHHcccC-CCCCEEEE
Confidence 456789999999 6888888888888999999554432 23335554
No 62
>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=50.74 E-value=40 Score=18.26 Aligned_cols=43 Identities=19% Similarity=0.146 Sum_probs=33.2
Q ss_pred EEEEEecCCeEEEEEcccCchhhhHHHHhcccCceeeeeeeEEE
Q psy11813 6 NVRVTTMDAELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQY 49 (70)
Q Consensus 6 ~~~V~lLD~~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y 49 (70)
.+.|..+.|...+++++.++-.+|-+++.+..++ ..+-+=|.|
T Consensus 2 ~i~vk~~~g~~~l~v~~~~TV~~lK~~I~~~~~i-~~~~~~Li~ 44 (71)
T cd01808 2 KVTVKTPKDKEEIEIAEDASVKDFKEAVSKKFKA-NQEQLVLIF 44 (71)
T ss_pred EEEEEcCCCCEEEEECCCChHHHHHHHHHHHhCC-CHHHEEEEE
Confidence 4567778886579999999999999999998885 455455555
No 63
>cd06401 PB1_TFG The PB1 domain found in TFG protein, an oncogenic gene product and fusion partner to nerve growth factor tyrosine kinase receptor TrkA and to the tyrosine kinase ALK. 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. The PB1 domains of TFG represent a type I/II PB1 domain. The physiological function of TFG remains unknown.
Probab=50.15 E-value=52 Score=19.42 Aligned_cols=50 Identities=18% Similarity=0.138 Sum_probs=36.2
Q ss_pred EEEEecCCeEEEEEccc-CchhhhHHHHhcccCc--eeeeeeeEEEecCCCCe
Q psy11813 7 VRVTTMDAELEFAIQHT-TTGKQLFDQTVKTIGL--REVWFFGLQYADSRGDL 56 (70)
Q Consensus 7 ~~V~lLD~~~~~~v~~~-~~G~~L~d~Vc~~L~L--~E~dYFGL~y~d~~~~~ 56 (70)
+++.+=++.-.+.++.. .+=.+|.+.+++-.+. .-.+.|.+.|.|.+|..
T Consensus 3 iK~~~g~DiR~~~~~~~~~t~~~L~~~v~~~F~~~~~~~~~flIKYkD~dGDl 55 (81)
T cd06401 3 LKAQLGDDIRRIPIHNEDITYDELLLMMQRVFRGKLGSSDDVLIKYKDEDGDL 55 (81)
T ss_pred EEEEeCCeEEEEeccCccccHHHHHHHHHHHhccccCCcccEEEEEECCCCCE
Confidence 45555455444777754 6888999999887774 34589999999987754
No 64
>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=47.96 E-value=49 Score=18.50 Aligned_cols=35 Identities=11% Similarity=0.030 Sum_probs=30.3
Q ss_pred EEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCc
Q psy11813 5 MNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGL 39 (70)
Q Consensus 5 ~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L 39 (70)
|.+.|.-+.| .+.+++++.++=.+|-+++.+.-++
T Consensus 2 ~~i~vkt~~Gk~~~~~v~~~~TV~~LK~~I~~~~~~ 37 (73)
T cd01791 2 IEVVCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGT 37 (73)
T ss_pred EEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHHhCC
Confidence 6788888888 7889999999999999999888774
No 65
>PRK15031 5-carboxymethyl-2-hydroxymuconate delta-isomerase; Provisional
Probab=47.87 E-value=12 Score=23.67 Aligned_cols=29 Identities=21% Similarity=0.407 Sum_probs=25.6
Q ss_pred cccCchhhhHHHHhcccC-ceeeeeeeEEE
Q psy11813 21 QHTTTGKQLFDQTVKTIG-LREVWFFGLQY 49 (70)
Q Consensus 21 ~~~~~G~~L~d~Vc~~L~-L~E~dYFGL~y 49 (70)
+++..|+.||+.+..++. +.++.|++|..
T Consensus 76 ~k~~l~~~l~~~l~~~~~~~~~~~~~~LS~ 105 (126)
T PRK15031 76 SRQEVGEMLFALIKAHFAALMESRYLALSF 105 (126)
T ss_pred HHHHHHHHHHHHHHHHhhhhhcccceEEEE
Confidence 467789999999999996 78999999998
No 66
>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=47.58 E-value=38 Score=17.92 Aligned_cols=30 Identities=13% Similarity=0.272 Sum_probs=26.6
Q ss_pred ecCC-eEEEEEcccCchhhhHHHHhcccCce
Q psy11813 11 TMDA-ELEFAIQHTTTGKQLFDQTVKTIGLR 40 (70)
Q Consensus 11 lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~ 40 (70)
.++| .+.+++.+.++-.+|=+.+.+..++.
T Consensus 2 ~~~g~~~~~~v~~~~tV~~lK~~i~~~~~~~ 32 (69)
T PF00240_consen 2 TLSGKTFTLEVDPDDTVADLKQKIAEETGIP 32 (69)
T ss_dssp ETTSEEEEEEEETTSBHHHHHHHHHHHHTST
T ss_pred CCCCcEEEEEECCCCCHHHhhhhcccccccc
Confidence 4678 78899999999999999999999964
No 67
>CHL00012 ndhJ NADH dehydrogenase subunit J
Probab=45.21 E-value=8.6 Score=25.31 Aligned_cols=32 Identities=13% Similarity=0.036 Sum_probs=23.4
Q ss_pred HHHhcccCceee---eeeeEEEecCCCCeecccCC
Q psy11813 31 DQTVKTIGLREV---WFFGLQYADSRGDLTWIKLY 62 (70)
Q Consensus 31 d~Vc~~L~L~E~---dYFGL~y~d~~~~~~WLd~~ 62 (70)
..++..-+-.|+ |.||+.|..+.+.++|+-++
T Consensus 101 ~~i~p~A~w~ERE~~DmfGI~F~GhPdlrrillpe 135 (158)
T CHL00012 101 FWVWKSADFQERESYDMLGISYDNHPRLKRILMPE 135 (158)
T ss_pred HHhhhCCChHHHHHHHHcCcccCCCCCCccccCCC
Confidence 344445555555 69999999999989988764
No 68
>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=44.84 E-value=48 Score=18.15 Aligned_cols=33 Identities=18% Similarity=0.097 Sum_probs=28.4
Q ss_pred EEEecCC-eEEEEEcccCchhhhHHHHhcccCce
Q psy11813 8 RVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLR 40 (70)
Q Consensus 8 ~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~ 40 (70)
.|..+.| ++.+.+++.++-.+|-+++.+..++.
T Consensus 2 ~vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gi~ 35 (74)
T cd01810 2 LVRNDKGRSSIYEVQLTQTVATLKQQVSQRERVQ 35 (74)
T ss_pred EEECCCCCEEEEEECCcChHHHHHHHHHHHhCCC
Confidence 4788888 78899999999999999998888864
No 69
>COG5227 SMT3 Ubiquitin-like protein (sentrin) [Posttranslational modification, protein turnover, chaperones]
Probab=44.04 E-value=50 Score=20.26 Aligned_cols=35 Identities=40% Similarity=0.515 Sum_probs=30.6
Q ss_pred eEEEEEEecCC-eEEEEEcccCchhhhHHHHhcccC
Q psy11813 4 LMNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIG 38 (70)
Q Consensus 4 ~~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~ 38 (70)
.+..+|.--|+ ++-|.|.+.++=+-|++..|++.|
T Consensus 24 hinLkvv~qd~telfFkiKktT~f~klm~af~~rqG 59 (103)
T COG5227 24 HINLKVVDQDGTELFFKIKKTTTFKKLMDAFSRRQG 59 (103)
T ss_pred ccceEEecCCCCEEEEEEeccchHHHHHHHHHHHhC
Confidence 46677877788 788999999999999999999987
No 70
>PF06100 Strep_67kDa_ant: Streptococcal 67 kDa myosin-cross-reactive antigen like family ; InterPro: IPR010354 Members of this family are thought to have structural features in common with the beta chain of the class II antigens, as well as myosin, and may play an important role in the pathogenesis [].
Probab=43.46 E-value=13 Score=28.63 Aligned_cols=21 Identities=14% Similarity=0.351 Sum_probs=18.7
Q ss_pred cCchhhhHHHHhcccCceeee
Q psy11813 23 TTTGKQLFDQTVKTIGLREVW 43 (70)
Q Consensus 23 ~~~G~~L~d~Vc~~L~L~E~d 43 (70)
.|+|+|++..++.||++.+..
T Consensus 409 eCtG~EIl~ElL~HLg~~~~~ 429 (500)
T PF06100_consen 409 ECTGEEILTELLYHLGFPDDE 429 (500)
T ss_pred hCChHHHHHHHHHhcCCChhh
Confidence 689999999999999997644
No 71
>KOG4261|consensus
Probab=42.72 E-value=16 Score=30.07 Aligned_cols=47 Identities=15% Similarity=0.196 Sum_probs=38.9
Q ss_pred ceEEEEEEecCCe-EEEEEcccCchhhhHHHHhcccCceeeeeeeEEE
Q psy11813 3 GLMNVRVTTMDAE-LEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQY 49 (70)
Q Consensus 3 ~~~~~~V~lLD~~-~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y 49 (70)
|....+|.||||. -.+.++-.-.+.+|.=.||+..||.+-+-.+|--
T Consensus 83 k~r~lkvrmldg~vkti~vd~sq~v~~L~~~ic~~igItnyeeyslvr 130 (1003)
T KOG4261|consen 83 KQRPLKVRMLDGAVKTIMVDDSQPVSQLMMTICNKIGITNYEEYSLVR 130 (1003)
T ss_pred hcccceeeecccccceeeecccccHHHHHHHHHhccCccchhhhhhhH
Confidence 4456789999995 4588888888999999999999999887667653
No 72
>cd01767 UBX UBX (ubiquitin regulatory X) domain. The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation.
Probab=42.11 E-value=61 Score=17.88 Aligned_cols=43 Identities=16% Similarity=0.037 Sum_probs=33.2
Q ss_pred EEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCceeeeeeeEEE
Q psy11813 5 MNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQY 49 (70)
Q Consensus 5 ~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y 49 (70)
..++|++.|| .+.-.....++=++|++-|-.+..- ..-|-|.-
T Consensus 3 t~i~iRlpdG~~~~~~F~~~~tl~~l~~fv~~~~~~--~~~f~L~t 46 (77)
T cd01767 3 TKIQIRLPDGKRLEQRFNSTHKLSDVRDFVESNGPP--AEPFTLMT 46 (77)
T ss_pred EEEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHcCCC--CCCEEEEe
Confidence 5689999999 6888888889999999999877643 34455553
No 73
>cd01772 SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-substrate-1), also known as Y33K, is a widely expressed protein containing N-terminal UBA (ubiquitin-associated) and C-terminal UBX (ubiqiutin-like) domains that was identified as a substrate of stress-activated protein kinases (SAPKs). SAKS1 is related evolutionarily to two other UBA/UBX-containing proteins, p47 and Faf1. The UBA and UBX domains of SAKS1 bind ubiquitin tetramers and valosin-containing protein (VCP), respectively suggesting a role for SAKS1 as an adaptor that directs VCP to polyubiquitinated proteins facilitating its destruction by the proteasome. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=39.68 E-value=71 Score=17.97 Aligned_cols=36 Identities=8% Similarity=0.040 Sum_probs=29.9
Q ss_pred ceEEEEEEecCC-eEEEEEcccCchhhhHHHHhcccC
Q psy11813 3 GLMNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIG 38 (70)
Q Consensus 3 ~~~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~ 38 (70)
....++|++.|| .+.-.....++=+++++-|..+.+
T Consensus 3 ~~~~i~iRlp~G~~~~~~F~~~~tl~~v~~fV~~~~~ 39 (79)
T cd01772 3 TETRIQIRLLDGTTLKQTFKAREQLAAVRLFVELNTG 39 (79)
T ss_pred cEEEEEEECCCCCEEEEEeCCCChHHHHHHHHHHcCC
Confidence 346789999999 677888888999999999987764
No 74
>PF01337 Barstar: Barstar (barnase inhibitor); InterPro: IPR000468 Barstar is a small single chain protein. Barnase is the extracellular ribonuclease IPR001887 from INTERPRO of Bacillus amyloliquefaciens, and barstar its specific intracellular inhibitor [, ]. Expression of barstar is necessary to counter the lethal effect of expressed active barnase. The structure of the barnase-barstar complex is known [].; PDB: 2CX6_A 1B2U_F 1A19_A 1X1U_F 1B27_E 1X1W_F 1BGS_E 1X1Y_D 1B3S_D 1B2S_D ....
Probab=39.66 E-value=23 Score=20.19 Aligned_cols=27 Identities=11% Similarity=0.350 Sum_probs=18.4
Q ss_pred EEEcccCchhhhHHHHhcccCceeeeeee
Q psy11813 18 FAIQHTTTGKQLFDQTVKTIGLREVWFFG 46 (70)
Q Consensus 18 ~~v~~~~~G~~L~d~Vc~~L~L~E~dYFG 46 (70)
++..+=.+-.++++.+.+.++++ +|||
T Consensus 3 idg~~i~~~~~~~~~l~~~l~fP--~yfG 29 (90)
T PF01337_consen 3 IDGRKIRDKEDFYDALAEALDFP--DYFG 29 (90)
T ss_dssp EECCC-SSHHHHHHHHHHHTT----TTSS
T ss_pred EeCCCCCCHHHHHHHHHHHcCCC--chhc
Confidence 44445556678899999999887 8888
No 75
>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=39.21 E-value=75 Score=18.06 Aligned_cols=46 Identities=13% Similarity=0.046 Sum_probs=35.5
Q ss_pred eEEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCceeeeeeeEEE
Q psy11813 4 LMNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQY 49 (70)
Q Consensus 4 ~~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y 49 (70)
...+.|.+.|| .+.-.+....+=++|++-|-.+.+-.+..-|-|..
T Consensus 4 ~t~iqiRlpdG~r~~~rF~~~~tv~~l~~~v~~~~~~~~~~~f~L~t 50 (79)
T cd01770 4 TTSIQIRLADGKRLVQKFNSSHRVSDVRDFIVNARPEFAARPFTLMT 50 (79)
T ss_pred eeEEEEECCCCCEEEEEeCCCCcHHHHHHHHHHhCCCCCCCCEEEec
Confidence 46789999999 67777778788889999999877544445677764
No 76
>cd01774 Faf1_like2_UBX Faf1 ike-2 UBX domain. Faf1_like2 is a protein of unknown function with a domain architecture that includes the UAS (ubiquitin-associated) and UBX (ubiquitin-like) domains. This protein is related to other UBA/UBX-containing proteins like Faf1, p47, and SAKS1 and may serve as an adaptor molecule that shuttles proteins to the proteasome for degradation. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=38.49 E-value=81 Score=18.24 Aligned_cols=45 Identities=9% Similarity=-0.005 Sum_probs=34.0
Q ss_pred ceEEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCceeeeeeeEEE
Q psy11813 3 GLMNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQY 49 (70)
Q Consensus 3 ~~~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y 49 (70)
....+.+.+.|| .++-......+=++|++-|..+.. +.+-|-|.+
T Consensus 3 ~~~~I~iRlp~G~Rl~rrF~~~~tl~~l~~fv~~~~~--~~~~f~L~t 48 (85)
T cd01774 3 DTVKIVFKLPNGTRVERRFLFTQSLRVIHDFLFSLKE--TPEKFQIVT 48 (85)
T ss_pred ceEEEEEECCCCCEEEEEeCCCCcHHHHHHHHHhCCC--CCCcEEEec
Confidence 457899999999 677778888899999999965443 224466655
No 77
>KOG2378|consensus
Probab=38.49 E-value=1.5e+02 Score=23.30 Aligned_cols=58 Identities=14% Similarity=0.185 Sum_probs=44.4
Q ss_pred eEEEEEEecCCe-EEEEEcccCchhhhHHHHhcccCceeeeeeeEEEecCCCCeecccCCC
Q psy11813 4 LMNVRVTTMDAE-LEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYADSRGDLTWIKLYK 63 (70)
Q Consensus 4 ~~~~~V~lLD~~-~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y~d~~~~~~WLd~~k 63 (70)
.+.|.|-+.|-+ +++.+.-.+..++++..|.+.++-.|- --|-=+.+.|.+.=|.|+.
T Consensus 235 ev~~~vy~~Dhsy~tl~~~vs~svqEI~~~va~k~~~see--l~LV~v~s~GEkv~lqPnd 293 (573)
T KOG2378|consen 235 EVFCIVYLPDHSYVTLRIRVSASVQEILEAVAEKLGYSEE--LILVKVSSSGEKVILQPND 293 (573)
T ss_pred eeeEEEEecCceEEEEEeechhHHHHHHHHHHHHhccccc--eeEEEEccCCceeeecCCc
Confidence 478999999985 569999999999999999999997665 2333356677776666543
No 78
>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=37.70 E-value=73 Score=17.53 Aligned_cols=33 Identities=18% Similarity=0.236 Sum_probs=28.2
Q ss_pred EEEecCC-eEEEEEcccCchhhhHHHHhcccCce
Q psy11813 8 RVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLR 40 (70)
Q Consensus 8 ~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~ 40 (70)
+|.++.| +..+++++.++=.++=.++.+.-++.
T Consensus 2 ~vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~gi~ 35 (70)
T cd01794 2 KVRLSTGKDVKLSVSSKDTVGQLKKQLQAAEGVD 35 (70)
T ss_pred eEEcCCCCEEEEEECCcChHHHHHHHHHHHhCCC
Confidence 6888988 78899999999999988888887763
No 79
>COG3232 HpaF 5-carboxymethyl-2-hydroxymuconate isomerase [Amino acid transport and metabolism]
Probab=37.17 E-value=14 Score=23.65 Aligned_cols=30 Identities=20% Similarity=0.380 Sum_probs=26.4
Q ss_pred cccCchhhhHHHHhcccC-ceeeeeeeEEEe
Q psy11813 21 QHTTTGKQLFDQTVKTIG-LREVWFFGLQYA 50 (70)
Q Consensus 21 ~~~~~G~~L~d~Vc~~L~-L~E~dYFGL~y~ 50 (70)
+++..|..||..+..|+. +.++-||+|.+.
T Consensus 76 ~rq~vge~Lf~~l~~~~A~l~a~r~lals~E 106 (127)
T COG3232 76 QRQEVGEALFAVLTAHFAPLFAQRYLALSFE 106 (127)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhccceeEEEE
Confidence 457789999999999995 899999999974
No 80
>PF00329 Complex1_30kDa: Respiratory-chain NADH dehydrogenase, 30 Kd subunit; InterPro: IPR001268 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 []. The 30 kDa subunit from NADH:ubiquinone oxidoreductase is found in both eukaryotes and prokaryotes. In mammals and in Neurospora crassa, it is nuclear-encoded as a precursor form with a transit peptide, while in Paramecium (protein P1), in the Dictyostelium discoideum (Slime mold) it is mitochondrial-encoded and it is chloroplast-encoded in various higher plants. It is also present in bacteria.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0055114 oxidation-reduction process; PDB: 2YBB_5 3IAS_E 2FUG_E 3I9V_5 3M9S_E 3IAM_5 3MCR_A.
Probab=37.13 E-value=7.4 Score=23.05 Aligned_cols=20 Identities=10% Similarity=0.121 Sum_probs=15.1
Q ss_pred eeeeEEEecCCCCeecccCC
Q psy11813 43 WFFGLQYADSRGDLTWIKLY 62 (70)
Q Consensus 43 dYFGL~y~d~~~~~~WLd~~ 62 (70)
|.||+.|.++.+.+.|+-++
T Consensus 75 DmfGI~f~GhPd~rrlll~~ 94 (103)
T PF00329_consen 75 DMFGIRFEGHPDLRRLLLPE 94 (103)
T ss_dssp HHCHHECCT-CCGS-SSSST
T ss_pred hhcCCEeCCCCCCccccCCC
Confidence 68999999988888887654
No 81
>PRK13977 myosin-cross-reactive antigen; Provisional
Probab=36.80 E-value=19 Score=28.14 Aligned_cols=19 Identities=21% Similarity=0.541 Sum_probs=17.3
Q ss_pred cCchhhhHHHHhcccCcee
Q psy11813 23 TTTGKQLFDQTVKTIGLRE 41 (70)
Q Consensus 23 ~~~G~~L~d~Vc~~L~L~E 41 (70)
.|+|+|++..+|-||++.+
T Consensus 427 ~CtG~Ei~~E~l~Hl~~~~ 445 (576)
T PRK13977 427 ECTGEEILQELLYHLGVPE 445 (576)
T ss_pred hCCHHHHHHHHHHhcCCch
Confidence 6899999999999999864
No 82
>PF02962 CHMI: 5-carboxymethyl-2-hydroxymuconate isomerase; InterPro: IPR004220 5-carboxymethyl-2-hydroxymuconate isomerase transforms 5-carboxymethyl-2-hydroxy-muconic acid into 5-oxo-pent-3-ene-1,2,5-tricarboxylic acid during the third step of the homoprotocatechuate catabolic pathway []. Homoprotocatechuate (HPC; 3,4-dihydroxyphenylacetate) is catabolized to Krebs cycle intermediates via extradiol (meta-) cleavage and the necessary enzymes are chromosomally encoded in a variety of bacteria []. 5-carboxymethyl-2-hydroxymuconate isomerase is probably a dimer of two identical subunits []. A comparison of the N-terminal half of the isomerase/decarboxylase sequence from the pathway (both encoded by the gene hpcE), with the second half showed significant similarity. This suggests that a duplication may have occurred to produce a bifunctional gene [].; PDB: 3E6Q_H 1OTG_B.
Probab=36.77 E-value=17 Score=22.90 Aligned_cols=29 Identities=14% Similarity=0.172 Sum_probs=24.6
Q ss_pred cccCchhhhHHHHhcccC-ceeeeeeeEEE
Q psy11813 21 QHTTTGKQLFDQTVKTIG-LREVWFFGLQY 49 (70)
Q Consensus 21 ~~~~~G~~L~d~Vc~~L~-L~E~dYFGL~y 49 (70)
+++..|+.||+.+.+++. +.+.-|++|..
T Consensus 75 ~k~~l~~~l~~~l~~~~~~~~~~~~~~Lsv 104 (124)
T PF02962_consen 75 QKKALSEALLAVLKAHLAPLFAQRYLQLSV 104 (124)
T ss_dssp HHHHHHHHHHHHHHHHCCCHCCHSEEEEEE
T ss_pred HHHHHHHHHHHHHHHHhhHhhcCCeeEEEE
Confidence 467789999999999987 57888999887
No 83
>PRK07785 NADH dehydrogenase subunit C; Provisional
Probab=35.23 E-value=18 Score=25.24 Aligned_cols=31 Identities=16% Similarity=0.048 Sum_probs=24.2
Q ss_pred HHHhcccCceee---eeeeEEEecCCCCeecccC
Q psy11813 31 DQTVKTIGLREV---WFFGLQYADSRGDLTWIKL 61 (70)
Q Consensus 31 d~Vc~~L~L~E~---dYFGL~y~d~~~~~~WLd~ 61 (70)
..|+-..+-.|+ |.||+.|..+.+.++||-+
T Consensus 166 t~I~P~A~W~EREvyDmfGI~FeGHPDLRRiLlp 199 (235)
T PRK07785 166 VSVYPTNDWHERETYDFFGIVFDGHPALTRIEMP 199 (235)
T ss_pred hhhcccCCchHHHHHHhcCceeCCCCCCccccCC
Confidence 445556666666 5999999999999999876
No 84
>smart00460 TGc Transglutaminase/protease-like homologues. Transglutaminases are enzymes that establish covalent links between proteins. A subset of transglutaminase homologues appear to catalyse the reverse reaction, the hydrolysis of peptide bonds. Proteins with this domain are both extracellular and intracellular, and it is likely that the eukaryotic intracellular proteins are involved in signalling events.
Probab=33.89 E-value=64 Score=16.68 Aligned_cols=34 Identities=18% Similarity=0.290 Sum_probs=25.0
Q ss_pred hhhHHHHhcccCceeeeeeeEEEec--------CCCCeeccc
Q psy11813 27 KQLFDQTVKTIGLREVWFFGLQYAD--------SRGDLTWIK 60 (70)
Q Consensus 27 ~~L~d~Vc~~L~L~E~dYFGL~y~d--------~~~~~~WLd 60 (70)
..+|..+|+.+|+.-+--+|..-.. ......|++
T Consensus 13 a~l~~~llr~~GIpar~v~g~~~~~~~~~~~~~~~~~H~W~e 54 (68)
T smart00460 13 AALFVALLRSLGIPARVVSGYLKAPDTIGGLRSIWEAHAWAE 54 (68)
T ss_pred HHHHHHHHHHCCCCeEEEeeeecCCCCCcccccCCCcEEEEE
Confidence 4578899999999999989976542 244555765
No 85
>KOG1769|consensus
Probab=33.76 E-value=1.2e+02 Score=18.65 Aligned_cols=38 Identities=26% Similarity=0.365 Sum_probs=32.5
Q ss_pred ceEEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCce
Q psy11813 3 GLMNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLR 40 (70)
Q Consensus 3 ~~~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~ 40 (70)
..+..+|.-=|+ ++.|.|.+++.=.-|.+.-|+.-|+.
T Consensus 19 ~hi~LKV~gqd~~~~~Fkikr~t~LkKLM~aYc~r~Gl~ 57 (99)
T KOG1769|consen 19 EHINLKVKGQDGSVVVFKIKRHTPLKKLMKAYCERQGLS 57 (99)
T ss_pred ceEEEEEecCCCCEEEEEeecCChHHHHHHHHHHHcCCc
Confidence 457888988555 67899999999999999999999874
No 86
>PF00762 Ferrochelatase: Ferrochelatase; InterPro: IPR001015 Synonym(s): Protohaem ferro-lyase, Iron chelatase, etc. Ferrochelatase catalyses the last step in haem biosynthesis: the chelation of a ferrous ion to proto-porphyrin IX, to form protohaem [, ]. In eukaryotic cells, it binds to the mitochondrial inner membrane with its active site on the matrix side of the membrane. The X-ray structure of Bacillus subtilis and human ferrochelatase have been solved [, ]. The human enzyme exists as a homodimer. Each subunit contains one [2Fe-2S] cluster. The monomer is folded into two similar domains, each with a four-stranded parallel beta-sheet flanked by an alpha-helix in a beta-alpha-beta motif that is reminiscent of the fold found in the periplasmic binding proteins. The topological similarity between the domains suggests that they have arisen from a gene duplication event. However, significant differences exist between the two domains, including an N-terminal section (residues 80-130) that forms part of the active site pocket, and a C-terminal extension (residues 390-423) that is involved in coordination of the [2Fe-2S] cluster and in stabilisation of the homodimer. Ferrochelatase seems to have a structurally conserved core region that is common to the enzyme from bacteria, plants and mammals. Porphyrin binds in the identified cleft; this cleft also includes the metal-binding site of the enzyme. It is likely that the structure of the cleft region will have different conformations upon substrate binding and release [].; GO: 0004325 ferrochelatase activity, 0006783 heme biosynthetic process; PDB: 2QD3_B 2HRE_C 3HCN_B 2PNJ_A 2QD1_C 1HRK_A 2QD4_B 3AQI_B 2HRC_B 3HCO_B ....
Probab=33.17 E-value=43 Score=23.89 Aligned_cols=31 Identities=19% Similarity=0.352 Sum_probs=23.5
Q ss_pred hHHHHhcccCceeeeeeeEEEecCCCCeecccCC
Q psy11813 29 LFDQTVKTIGLREVWFFGLQYADSRGDLTWIKLY 62 (70)
Q Consensus 29 L~d~Vc~~L~L~E~dYFGL~y~d~~~~~~WLd~~ 62 (70)
-.+.|.+++++.+ .-+.|++.-+...||.|+
T Consensus 212 t~~~i~~~l~~~~---~~~~fQS~~g~~~WL~P~ 242 (316)
T PF00762_consen 212 TARLIAERLGLPE---WRLAFQSRFGPGEWLGPS 242 (316)
T ss_dssp HHHHHHHHTTTSS---EEEEEES-SSSS-BSSSB
T ss_pred HHHHHHHHcCCCc---eEEEEECCCCCCCCcccc
Confidence 3467888888887 788999888888999875
No 87
>cd02639 R3H_RRM R3H domain of mainly fungal proteins which are associated with a RNA recognition motif (RRM) domain. Present in this group is the RNA-binding post-transcriptional regulator Cip2 (Csx1-interacting protein 2) involved in counteracting Csx1 function. Csx1 plays a central role in controlling gene expression during oxidative stress. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=32.17 E-value=44 Score=18.41 Aligned_cols=27 Identities=19% Similarity=0.357 Sum_probs=20.6
Q ss_pred EEEEcc--cCchhhhHHHHhcccCceeee
Q psy11813 17 EFAIQH--TTTGKQLFDQTVKTIGLREVW 43 (70)
Q Consensus 17 ~~~v~~--~~~G~~L~d~Vc~~L~L~E~d 43 (70)
++..++ ...-+-++-.+|..|||.++.
T Consensus 19 eL~Fp~~ls~~eRriih~la~~lGL~~~s 47 (60)
T cd02639 19 ELAFPSSLSPAERRIVHLLASRLGLNHVS 47 (60)
T ss_pred EEEcCCCCCHHHHHHHHHHHHHcCCceEE
Confidence 344454 455788999999999999884
No 88
>PRK12435 ferrochelatase; Provisional
Probab=31.24 E-value=48 Score=23.66 Aligned_cols=30 Identities=7% Similarity=0.236 Sum_probs=22.5
Q ss_pred HHHHhcccCceeeeeeeEEEecC-CCCeecccCC
Q psy11813 30 FDQTVKTIGLREVWFFGLQYADS-RGDLTWIKLY 62 (70)
Q Consensus 30 ~d~Vc~~L~L~E~dYFGL~y~d~-~~~~~WLd~~ 62 (70)
-..|++.|++.+ +-+.|++. .+...||.|+
T Consensus 203 ~~~v~~~l~~~~---~~l~yQSr~~g~~~WL~P~ 233 (311)
T PRK12435 203 ADLIAEQANVEH---YAIGWQSEGNTPDPWLGPD 233 (311)
T ss_pred HHHHHHHcCCCC---CeEeeecCCCCCCCCCCCC
Confidence 456778888753 67999987 3567899885
No 89
>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=29.96 E-value=1.2e+02 Score=17.72 Aligned_cols=45 Identities=11% Similarity=0.116 Sum_probs=33.8
Q ss_pred EEEEcccCchhhhHHHHhcccCceeeeeeeEEEecCCCCeecccCC
Q psy11813 17 EFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYADSRGDLTWIKLY 62 (70)
Q Consensus 17 ~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y~d~~~~~~WLd~~ 62 (70)
-+.+++.+.=.+|.++|.+.|.+.... =-|.|.+......|+.+.
T Consensus 10 ai~v~~g~~y~~L~~~ls~kL~l~~~~-~~LSY~~~~~~~~~v~l~ 54 (78)
T cd06411 10 ALRAPRGADVSSLRALLSQALPQQAQR-GQLSYRAPGEDGHWVPIS 54 (78)
T ss_pred EEEccCCCCHHHHHHHHHHHhcCChhh-cEEEecCCCCCccEeecC
Confidence 355678888889999999999986544 468888776655786654
No 90
>PRK08491 NADH dehydrogenase subunit C; Provisional
Probab=29.45 E-value=25 Score=24.90 Aligned_cols=32 Identities=13% Similarity=-0.025 Sum_probs=25.0
Q ss_pred HHHhcccCceee---eeeeEEEecCCCCeecccCC
Q psy11813 31 DQTVKTIGLREV---WFFGLQYADSRGDLTWIKLY 62 (70)
Q Consensus 31 d~Vc~~L~L~E~---dYFGL~y~d~~~~~~WLd~~ 62 (70)
..++..-+..|+ |.||+.|..+.+.++||-++
T Consensus 129 t~IfpsAnW~ERE~~DMFGI~FeGHPDlRRiLLpe 163 (263)
T PRK08491 129 SFLFKSANWSEREMYDMFGIVINNHPYLKRILMPD 163 (263)
T ss_pred HHhhhcCCchHHHHHHhhCceeCCCCCCcccCCCC
Confidence 455566667676 59999999999999988765
No 91
>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=29.31 E-value=1e+02 Score=16.74 Aligned_cols=35 Identities=9% Similarity=0.060 Sum_probs=29.0
Q ss_pred EEEec-CC-eEEEEEcccCchhhhHHHHhcccCceee
Q psy11813 8 RVTTM-DA-ELEFAIQHTTTGKQLFDQTVKTIGLREV 42 (70)
Q Consensus 8 ~V~lL-D~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~ 42 (70)
.|.++ .| ++.+.+++..+=.+|-.++.+.-|+...
T Consensus 2 ~v~~~~~g~~~~l~v~~~~TV~~lK~~I~~~~gip~~ 38 (71)
T cd01796 2 TVYTARSETTFSLDVDPDLELENFKALCEAESGIPAS 38 (71)
T ss_pred EEEECCCCCEEEEEECCcCCHHHHHHHHHHHhCCCHH
Confidence 57788 77 6889999999989999999988887543
No 92
>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=28.48 E-value=1.2e+02 Score=17.05 Aligned_cols=44 Identities=23% Similarity=0.238 Sum_probs=32.4
Q ss_pred EEEEEEecCC-e-EEEE-EcccCchhhhHHHHhcccCceeeeeeeEEE
Q psy11813 5 MNVRVTTMDA-E-LEFA-IQHTTTGKQLFDQTVKTIGLREVWFFGLQY 49 (70)
Q Consensus 5 ~~~~V~lLD~-~-~~~~-v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y 49 (70)
|.+.|..+.| + ..++ +++..+=.++-+++.+..++. .+-.-|.|
T Consensus 1 M~I~vk~~~G~~~~~l~~v~~~~TV~~lK~~i~~~~gi~-~~~QrLi~ 47 (78)
T cd01797 1 MWIQVRTMDGKETRTVDSLSRLTKVEELREKIQELFNVE-PECQRLFY 47 (78)
T ss_pred CEEEEEcCCCCEEEEeeccCCcCcHHHHHHHHHHHhCCC-HHHeEEEe
Confidence 5788999999 4 4674 788888889999999988853 34344444
No 93
>cd01771 Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated factor1) is a nucleolar protein that was first identified as an interaction partner of the death receptor Fas. Faf1 contains N-terminal UAS (ubiquitin-associated) and C-terminal UBX (ubiquitin-like) domains and is closely related to other UBA/UBX-containing proteins like p47, Rep8 and SAKS1. Faf1 is thought to be involved in 18S rRNA synthesis and/or 40S ribosomal subunit assembly. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=28.19 E-value=1.2e+02 Score=17.24 Aligned_cols=43 Identities=21% Similarity=0.169 Sum_probs=31.9
Q ss_pred eEEEEEEecCC-eEEEEEcccCchhhhHHHHhcccCceeeeeeeEE
Q psy11813 4 LMNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQ 48 (70)
Q Consensus 4 ~~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~ 48 (70)
...++|.+.|| .++-.....++=++|++-|-.+ +- +.+-|-|.
T Consensus 4 ~~~i~iRlP~G~r~~rrF~~t~~L~~l~~fv~~~-~~-~~~~f~L~ 47 (80)
T cd01771 4 ISKLRVRTPSGDFLERRFLGDTPLQVLLNFVASK-GY-PIDEYKLL 47 (80)
T ss_pred eEEEEEECCCCCEEEEEeCCCCcHHHHHHHHHhc-CC-CCCCEEEe
Confidence 46789999999 6778888888989999999654 22 23355554
No 94
>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=27.10 E-value=1.3e+02 Score=22.27 Aligned_cols=34 Identities=18% Similarity=0.309 Sum_probs=29.5
Q ss_pred EEEEEEecCC-eEEEEEcccCchhhhHHHHhcccC
Q psy11813 5 MNVRVTTMDA-ELEFAIQHTTTGKQLFDQTVKTIG 38 (70)
Q Consensus 5 ~~~~V~lLD~-~~~~~v~~~~~G~~L~d~Vc~~L~ 38 (70)
|.+.|..+++ .+.++|++..+-.+|-.++...-+
T Consensus 1 MkItVKtl~g~~~~IeV~~~~TV~dLK~kI~~~~g 35 (378)
T TIGR00601 1 MTLTFKTLQQQKFKIDMEPDETVKELKEKIEAEQG 35 (378)
T ss_pred CEEEEEeCCCCEEEEEeCCcChHHHHHHHHHHhhC
Confidence 5788999999 788999999999999888888765
No 95
>PF14533 USP7_C2: Ubiquitin-specific protease C-terminal; PDB: 2YLM_A.
Probab=26.22 E-value=56 Score=21.88 Aligned_cols=37 Identities=27% Similarity=0.439 Sum_probs=22.5
Q ss_pred EEEEEecC-C-----eEEEEEcccCchhhhHHHHhcccCceee
Q psy11813 6 NVRVTTMD-A-----ELEFAIQHTTTGKQLFDQTVKTIGLREV 42 (70)
Q Consensus 6 ~~~V~lLD-~-----~~~~~v~~~~~G~~L~d~Vc~~L~L~E~ 42 (70)
.++|..+. + ++++.+++.++=++|++.+.+.+++.|.
T Consensus 20 ~~kv~w~~~~~~~~~~~~~~vpk~~tV~Dll~~l~~k~~~~~~ 62 (213)
T PF14533_consen 20 QFKVTWLNDGLKEEQEYELLVPKTGTVSDLLEELQKKVGFSEE 62 (213)
T ss_dssp -EEEEEE-TTS-EE-EEEE--BTT-BHHHHHHHHHTT----TT
T ss_pred EEEEEEECCCCcceeEEEEEECCCCCHHHHHHHHHHHcCCCcC
Confidence 46666663 3 2568889999999999999999998664
No 96
>cd06403 PB1_Par6 The PB1 domain is an essential part of Par6 protein which in complex with Par3 and aPKC proteins is crucial for establishment of apical-basal polarity of animal cells. The 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
Probab=25.91 E-value=1.5e+02 Score=17.49 Aligned_cols=43 Identities=28% Similarity=0.417 Sum_probs=27.2
Q ss_pred CCeE-EEEEcccCchhh-hHHHHhcccCceeeeeeeEEEecCCCC
Q psy11813 13 DAEL-EFAIQHTTTGKQ-LFDQTVKTIGLREVWFFGLQYADSRGD 55 (70)
Q Consensus 13 D~~~-~~~v~~~~~G~~-L~d~Vc~~L~L~E~dYFGL~y~d~~~~ 55 (70)
|++. .|.++++..|+. =|-...+++.-+...-|=+.|+|..|.
T Consensus 8 daEfRRFsl~r~~~~~f~ef~~ll~~lH~l~~~~f~i~Y~D~~gD 52 (80)
T cd06403 8 DAEFRRFSLDRNKPGKFEDFYKLLEHLHHIPNVDFLIGYTDPHGD 52 (80)
T ss_pred CCeEEEEEeccccCcCHHHHHHHHHHHhCCCCCcEEEEEeCCCCC
Confidence 4554 489988754432 244444555555557789999998654
No 97
>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=25.81 E-value=1.2e+02 Score=16.63 Aligned_cols=29 Identities=17% Similarity=0.257 Sum_probs=24.5
Q ss_pred cCC-eEEEEEcccCchhhhHHHHhcccCce
Q psy11813 12 MDA-ELEFAIQHTTTGKQLFDQTVKTIGLR 40 (70)
Q Consensus 12 LD~-~~~~~v~~~~~G~~L~d~Vc~~L~L~ 40 (70)
|+| ++++++++.++-.++=+++-...++.
T Consensus 5 l~g~~~~l~v~~~~TV~~lK~~i~~~~gip 34 (76)
T cd01800 5 LNGQMLNFTLQLSDPVSVLKVKIHEETGMP 34 (76)
T ss_pred cCCeEEEEEECCCCcHHHHHHHHHHHHCCC
Confidence 567 67899999999999999998888763
No 98
>PF07865 DUF1652: Protein of unknown function (DUF1652); InterPro: IPR012448 The proteins in this entry have not been characterised.
Probab=25.80 E-value=59 Score=18.50 Aligned_cols=25 Identities=8% Similarity=0.194 Sum_probs=18.8
Q ss_pred eEEEEEEecCC-eEEEEEcccCchhh
Q psy11813 4 LMNVRVTTMDA-ELEFAIQHTTTGKQ 28 (70)
Q Consensus 4 ~~~~~V~lLD~-~~~~~v~~~~~G~~ 28 (70)
++.|..++.++ ++++.+-...+|++
T Consensus 14 Pl~C~ct~~~~~smtvrl~d~~sg~~ 39 (69)
T PF07865_consen 14 PLRCECTIAPDGSMTVRLFDPASGRV 39 (69)
T ss_pred CceeEEEECCCCcEEEEEecCCCCcE
Confidence 46788888887 78888777777766
No 99
>PF14039 YusW: YusW-like protein
Probab=25.71 E-value=36 Score=20.31 Aligned_cols=30 Identities=23% Similarity=0.377 Sum_probs=21.4
Q ss_pred EEEcccCchhhhHHHHhcccCcee-eeeeeE
Q psy11813 18 FAIQHTTTGKQLFDQTVKTIGLRE-VWFFGL 47 (70)
Q Consensus 18 ~~v~~~~~G~~L~d~Vc~~L~L~E-~dYFGL 47 (70)
+.+++.+.-+++.++|.+.++|.+ -+-|-|
T Consensus 56 L~~~~~t~~~evi~~Vl~~f~Ld~dy~~fel 86 (92)
T PF14039_consen 56 LSFDSDTSEEEVIDQVLKAFNLDPDYQEFEL 86 (92)
T ss_pred CCCCCCCChHHHHHHHHHHhCCCccceEEEE
Confidence 556677777888899999999864 333444
No 100
>cd03590 CLECT_DC-SIGN_like C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR). CLECT_DC-SIGN_like: C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR). This group also contains proteins similar to hepatic asialoglycoprotein receptor (ASGP-R) and langerin in human. These proteins are type II membrane proteins with a CTLD ectodomain. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. DC-SIGN is thought to mediate the initial contact between dendritic cells and resting T cells, and may also mediate the rolling of DCs on epithelium. DC-SIGN and DC-SIGNR bind to oligosaccharides present on human tissues, as well as, on path
Probab=25.17 E-value=1e+02 Score=17.66 Aligned_cols=33 Identities=15% Similarity=0.410 Sum_probs=21.9
Q ss_pred HHHhcccCceeeeeeeEEEecCCCCeecccCCC
Q psy11813 31 DQTVKTIGLREVWFFGLQYADSRGDLTWIKLYK 63 (70)
Q Consensus 31 d~Vc~~L~L~E~dYFGL~y~d~~~~~~WLd~~k 63 (70)
+.|.+.+.-...-+.||......+...|+|...
T Consensus 46 ~~l~~~~~~~~~~WiGl~~~~~~~~~~W~dg~~ 78 (126)
T cd03590 46 EFISKILSGNRSYWIGLSDEETEGEWKWVDGTP 78 (126)
T ss_pred HHHHHHhCCCCCEEEeeecCCCcCCeEecCCCC
Confidence 334444433456688999877788899988543
No 101
>PF15152 Kisspeptin: Kisspeptin
Probab=25.13 E-value=23 Score=20.86 Aligned_cols=6 Identities=67% Similarity=1.337 Sum_probs=5.0
Q ss_pred eeeEEE
Q psy11813 44 FFGLQY 49 (70)
Q Consensus 44 YFGL~y 49 (70)
-|||+|
T Consensus 72 SFGLRY 77 (78)
T PF15152_consen 72 SFGLRY 77 (78)
T ss_pred cccccc
Confidence 699988
No 102
>TIGR02582 cas_TM1809 CRISPR-associated RAMP protein, Csm3 family. Members of this CRISPR-associated (cas) gene family are found in the mtube subtype of CRISPR/cas locus and designated Csm3, for CRISPR/cas Subtype Mtube, protein 3.
Probab=24.90 E-value=55 Score=21.98 Aligned_cols=22 Identities=18% Similarity=0.243 Sum_probs=18.1
Q ss_pred hhhhHHHHhcccCceeeeeeeE
Q psy11813 26 GKQLFDQTVKTIGLREVWFFGL 47 (70)
Q Consensus 26 G~~L~d~Vc~~L~L~E~dYFGL 47 (70)
-.+.|..+..-|.+.|.+|+|=
T Consensus 172 ~~~~~~~l~~~l~lle~~~LGg 193 (204)
T TIGR02582 172 EEEDFKNILEGLKLLEDDYLGG 193 (204)
T ss_pred HHHHHHHHHHHHHhhccCccCC
Confidence 4467889999999999999874
No 103
>COG0276 HemH Protoheme ferro-lyase (ferrochelatase) [Coenzyme metabolism]
Probab=24.73 E-value=83 Score=22.92 Aligned_cols=35 Identities=20% Similarity=0.452 Sum_probs=28.5
Q ss_pred hhhHHHHhcccCceeeeeeeEEEecCCCCeecccCC
Q psy11813 27 KQLFDQTVKTIGLREVWFFGLQYADSRGDLTWIKLY 62 (70)
Q Consensus 27 ~~L~d~Vc~~L~L~E~dYFGL~y~d~~~~~~WLd~~ 62 (70)
++-...|.+.|++.+.+| -+.|++..+.--||.|+
T Consensus 210 ~~t~~li~e~lg~~~~~~-~~~~QS~~G~~~WL~P~ 244 (320)
T COG0276 210 QETTRLIAEALGLPEEEY-DLTFQSRFGPEPWLQPY 244 (320)
T ss_pred HHHHHHHHHHcCCCchhe-eEEeecCCCCCCCCCCC
Confidence 455778999999976664 68999888999999875
No 104
>cd05141 Barstar_evA4336-like Barstar_evA4336-like contains uncharacterized sequences similar to the uncharacterized, predicted RNAase inhibitor evA4336 found in Azoarcus sp. EvN1. This is a subfamily of the Barstar family of RNAase inhibitors. Barstar is an intracellular inhibitor of barnase, an extracellular ribonuclease of Bacillus amyloliquefaciens. Barstar binds tightly to the barnase active site and sterically blocks it thus inhibiting its potentially lethal RNase activity inside the cell. Barstar also binds and inhibits a ribonuclease called RNase Sa (produced by Streptomyces aureofaciens) which belongs to the same enzyme family as does barnase.
Probab=24.31 E-value=68 Score=18.18 Aligned_cols=26 Identities=15% Similarity=0.347 Sum_probs=18.5
Q ss_pred EEcccCchhhhHHHHhcccCceeeeeee
Q psy11813 19 AIQHTTTGKQLFDQTVKTIGLREVWFFG 46 (70)
Q Consensus 19 ~v~~~~~G~~L~d~Vc~~L~L~E~dYFG 46 (70)
...+-.+=.++++.+.+.++.+ +|||
T Consensus 4 dg~~i~~~~~~~~~l~~~l~fP--~yfG 29 (81)
T cd05141 4 DLSGIADKAALLDALAAALDFP--SWFG 29 (81)
T ss_pred ecccCCCHHHHHHHHHHHcCCC--cccc
Confidence 3344445667888888888766 7888
No 105
>PF01841 Transglut_core: Transglutaminase-like superfamily; InterPro: IPR002931 This domain is found in many proteins known to have transglutaminase activity, i.e. which cross-link proteins through an acyl-transfer reaction between the gamma-carboxamide group of peptide-bound glutamine and the epsilon-amino group of peptide-bound lysine, resulting in a epsilon-(gamma-glutamyl)lysine isopeptide bond. Tranglutaminases have been found in a diverse range of species, from bacteria through to mammals. The enzymes require calcium binding and their activity leads to post-translational modification of proteins through acyl-transfer reactions, involving peptidyl glutamine residues as acyl donors and a variety of primary amines as acyl acceptors, with the generation of proteinase resistant isopeptide bonds []. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterised transglutaminase, the human blood clotting factor XIIIa' []. On the basis of the experimentally demonstrated activity of the Methanobacterium phage psiM2 pseudomurein endoisopeptidase [], it is proposed that many, if not all, microbial homologs of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease []. A subunit of plasma Factor XIII revealed that each Factor XIIIA subunit is composed of four domains (termed N-terminal beta-sandwich, core domain (containing the catalytic and the regulatory sites), and C-terminal beta-barrels 1 and 2) and that two monomers assemble into the native dimer through the surfaces in domains 1 and 2, in opposite orientation. This organisation in four domains is highly conserved during evolution among transglutaminase isoforms [].; PDB: 2F4M_A 2F4O_A 1GGY_B 1FIE_B 1GGU_B 1GGT_B 1F13_A 1QRK_B 1EVU_A 1EX0_B ....
Probab=24.25 E-value=58 Score=18.48 Aligned_cols=24 Identities=17% Similarity=0.266 Sum_probs=18.3
Q ss_pred hhhHHHHhcccCceeeeeeeEEEe
Q psy11813 27 KQLFDQTVKTIGLREVWFFGLQYA 50 (70)
Q Consensus 27 ~~L~d~Vc~~L~L~E~dYFGL~y~ 50 (70)
..||..+|+.+|+.-+--+|....
T Consensus 58 a~l~~allr~~Gipar~v~g~~~~ 81 (113)
T PF01841_consen 58 ASLFVALLRALGIPARVVSGYVKG 81 (113)
T ss_dssp HHHHHHHHHHHT--EEEEEEEEEE
T ss_pred HHHHHHHHhhCCCceEEEEEEcCC
Confidence 457899999999999888887764
No 106
>PRK11615 hypothetical protein; Provisional
Probab=24.11 E-value=70 Score=21.73 Aligned_cols=19 Identities=21% Similarity=0.438 Sum_probs=15.5
Q ss_pred EEEEecCCeEEEEEcccCc
Q psy11813 7 VRVTTMDAELEFAIQHTTT 25 (70)
Q Consensus 7 ~~V~lLD~~~~~~v~~~~~ 25 (70)
-.|+||||.+.|.++..-.
T Consensus 41 q~VSLLdGKl~FtLPag~s 59 (185)
T PRK11615 41 QPVSLLDGKLSFTLPADMS 59 (185)
T ss_pred ceeEEeccEEEEEcCCccc
Confidence 3799999999999987443
No 107
>PF13718 GNAT_acetyltr_2: GNAT acetyltransferase 2; PDB: 2ZPA_B.
Probab=23.17 E-value=78 Score=21.39 Aligned_cols=30 Identities=20% Similarity=0.276 Sum_probs=21.2
Q ss_pred cccCchhhhHHHHhcccC-------------------------ceeeeeeeEEEe
Q psy11813 21 QHTTTGKQLFDQTVKTIG-------------------------LREVWFFGLQYA 50 (70)
Q Consensus 21 ~~~~~G~~L~d~Vc~~L~-------------------------L~E~dYFGL~y~ 50 (70)
+....|..+++.+-++.+ -...||+|..|-
T Consensus 103 q~~G~Gs~lL~~l~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~vDylGtSFG 157 (196)
T PF13718_consen 103 QRMGYGSRLLQQLEQYAEGKIPSLSEQDKEKLPPLLSKLSDRRPPGVDYLGTSFG 157 (196)
T ss_dssp -SSSHHHHHHHHHHHT-----------------------------S-SEEEEEEE
T ss_pred hcCCHHHHHHHHHHHHHhhhcccccccccccccccccccccccccCCCEEEeccC
Confidence 456779999999999994 567899999993
No 108
>cd07762 CYTH-like_Pase_1 Uncharacterized subgroup 1 of the CYTH-like superfamily. Enzymes belonging to the CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) superfamily hydrolyze triphosphate-containing substrates, require metal cations as cofactors, and have a unique active site located at the center of an eight-stranded antiparallel beta barrel tunnel (the triphosphate tunnel). The name CYTH originated from the gene designation for bacterial class IV adenylyl cyclases (CyaB) and from thiamine triphosphatase. Class IV adenylate cyclases catalyze the conversion of ATP to 3',5'-cyclic AMP (cAMP) and PPi. Thiamine triphosphatase is a soluble cytosolic enzyme which converts thiamine triphosphate to thiamine diphosphate. This domain superfamily also contains RNA triphosphatases, membrane-associated polyphosphate polymerases, tripolyphosphatases, nucleoside triphosphatases, nucleoside tetraphosphatases and other proteins with unknown functions. Proteins of this subgroup
Probab=22.74 E-value=1e+02 Score=20.06 Aligned_cols=25 Identities=24% Similarity=0.478 Sum_probs=18.8
Q ss_pred EEEEEcccCchhhhHHHHhcccCce
Q psy11813 16 LEFAIQHTTTGKQLFDQTVKTIGLR 40 (70)
Q Consensus 16 ~~~~v~~~~~G~~L~d~Vc~~L~L~ 40 (70)
+|+.++....|+..|..+.+.+|+.
T Consensus 144 lE~e~~~~~~~~~~~~~ll~~~gi~ 168 (180)
T cd07762 144 LEYEVDDYEAGKKAFLELLKQYNIP 168 (180)
T ss_pred EEEEeCCHHHHHHHHHHHHHHcCCC
Confidence 3455555568999999999998764
No 109
>COG5605 Predicted small integral membrane protein [Function unknown]
Probab=22.74 E-value=14 Score=22.79 Aligned_cols=7 Identities=71% Similarity=1.123 Sum_probs=5.8
Q ss_pred eeeeeEE
Q psy11813 42 VWFFGLQ 48 (70)
Q Consensus 42 ~dYFGL~ 48 (70)
.||||||
T Consensus 39 vdyfglq 45 (115)
T COG5605 39 VDYFGLQ 45 (115)
T ss_pred HHHHhhh
Confidence 5899987
No 110
>PF12380 Peptidase_C62: Gill-associated viral 3C-like peptidase; InterPro: IPR024348 This protease is found in polyproteins from the positive-stranded RNA virus of prawns called yellow head virus or gill-associated virus (GAV). The GAV cysteine proteinase (3C-like proteinase) is predicted to be the key enzyme in the processing of the GAV replicase polyprotein precursors, polyprotein 1a and polyprotein 1ab. This protease employs a Cys(2968)-His(2879) catalytic dyad []. It is classified as family C62 in the MEROPS database.
Probab=22.48 E-value=94 Score=21.59 Aligned_cols=44 Identities=25% Similarity=0.482 Sum_probs=29.8
Q ss_pred cCchhhhHHHHhcccCceeeeeeeEEEecC-CCCeecccCCCeecCCCC
Q psy11813 23 TTTGKQLFDQTVKTIGLREVWFFGLQYADS-RGDLTWIKLYKKVRCPNN 70 (70)
Q Consensus 23 ~~~G~~L~d~Vc~~L~L~E~dYFGL~y~d~-~~~~~WLd~~k~i~~~~~ 70 (70)
..-|..+||..-+ ..-....|+.-.-+ ++...| ++++++.|+||
T Consensus 144 gdcgs~~fdhl~n---vvgahivgi~~ippvngaltw-n~e~e~lcgpn 188 (284)
T PF12380_consen 144 GDCGSIIFDHLHN---VVGAHIVGISCIPPVNGALTW-NPEKEMLCGPN 188 (284)
T ss_pred CCcchhHHHhhhc---cccceeEEeeccCCCCcceec-CcccccccCCC
Confidence 3346666664433 44456678877544 577789 88999999987
No 111
>cd06901 lectin_VIP36_VIPL VIP36 and VIPL type 1 transmembrane proteins, lectin domain. The vesicular integral protein of 36 kDa (VIP36) is a type 1 transmembrane protein of the mammalian early secretory pathway that acts as a cargo receptor transporting high mannose type glycoproteins between the Golgi and the endoplasmic reticulum (ER). Lectins of the early secretory pathway are involved in the selective transport of newly synthesized glycoproteins from the ER to the ER-Golgi intermediate compartment (ERGIC). The most prominent cycling lectin is the mannose-binding type1 membrane protein ERGIC-53, which functions as a cargo receptor to facilitate export of glycoproteins from the ER. L-type lectins have a dome-shaped beta-barrel carbohydrate recognition domain with a curved seven-stranded beta-sheet referred to as the "front face" and a flat six-stranded beta-sheet referred to as the "back face". This domain homodimerizes so that adjacent back sheets form a contiguous 12-stranded she
Probab=21.71 E-value=1.2e+02 Score=20.96 Aligned_cols=44 Identities=18% Similarity=0.274 Sum_probs=27.1
Q ss_pred EEEEEecCCeEEEEEcccCchh--hhHHHHhcccCceeeeeeeEEEec
Q psy11813 6 NVRVTTMDAELEFAIQHTTTGK--QLFDQTVKTIGLREVWFFGLQYAD 51 (70)
Q Consensus 6 ~~~V~lLD~~~~~~v~~~~~G~--~L~d~Vc~~L~L~E~dYFGL~y~d 51 (70)
.++++-..+.+++.++.+..|. .||+. +...|...-|||+.=..
T Consensus 161 ~~rI~Y~~~~l~v~vd~~~~~~w~~Cf~~--~~v~LP~~~yfGiSA~T 206 (248)
T cd06901 161 FVAIRYSKGRLTVMTDIDGKNEWKECFDV--TGVRLPTGYYFGASAAT 206 (248)
T ss_pred EEEEEEECCeEEEEEecCCCCceeeeEEe--CCeecCCCCEEEEEecC
Confidence 4566666565555555444444 55544 55667888899987643
No 112
>PF00794 PI3K_rbd: PI3-kinase family, ras-binding domain; InterPro: IPR000341 Phosphatidylinositol 3-kinase (PI3K) (2.7.1.137 from EC) is an enzyme that phosphorylates phosphoinositides on the 3-hydroxyl group of the inositol ring. A subset of PI3Ks has the capacity to bind and be activated by the GTP-bound small GTPase p21Ras (Ras). PI3Ks are recognised as one of the principal effectors of Ras signalling to the cell-cycle control machinery. In the structure of the Ras-PI3K gamma complex, contacts between the two molecules are made primarily via the so-called switch I region of Ras and the PI3K RBD. The RBD fold comprises a five-stranded mixed beta-sheet, flanked by two alpha-helices. Interaction between Ras and the PI3K RBD is primarily polar in character and, as characterised by kinetic measurements, is reversible and transient [].; GO: 0016303 1-phosphatidylinositol-3-kinase activity, 0005942 phosphatidylinositol 3-kinase complex; PDB: 2RD0_A 3HIZ_A 3HHM_A 1E8W_A 1E8X_A 1E7V_A 1E90_A 1E7U_A 2Y3A_A 3L54_A ....
Probab=21.66 E-value=1.8e+02 Score=16.96 Aligned_cols=48 Identities=17% Similarity=0.222 Sum_probs=34.8
Q ss_pred ceEEEEEEecCC--eEEEEEcccCchhhhHHHHhcc----cCceeee-eeeEEEe
Q psy11813 3 GLMNVRVTTMDA--ELEFAIQHTTTGKQLFDQTVKT----IGLREVW-FFGLQYA 50 (70)
Q Consensus 3 ~~~~~~V~lLD~--~~~~~v~~~~~G~~L~d~Vc~~----L~L~E~d-YFGL~y~ 50 (70)
..+.+.|...++ ...|.++.+++-.+|...+.+. ++..+.. =|-|+..
T Consensus 15 ~~i~v~v~~~~~~~~~t~~~~~~~t~~~li~~~l~k~~~~~~~~~~~~dyvLKV~ 69 (106)
T PF00794_consen 15 NKIKVSVHFENSQQSFTFQVDPNSTPEELIAQALKKKLKDLLPPDPEDDYVLKVC 69 (106)
T ss_dssp SEEEEEEEETTCSEEEEEEEETTS-HHHHHHHHHHHHHHHTT-CHHHHGEEEEET
T ss_pred CeEEEEEEEcCCCcEEEEEECCCCCHHHHHHHHHHHHHhhcCCcccccCEEEEec
Confidence 457888998854 5779999999999999988887 3344444 5777765
No 113
>PRK11742 bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional
Probab=20.99 E-value=46 Score=25.89 Aligned_cols=32 Identities=9% Similarity=0.030 Sum_probs=24.6
Q ss_pred HHHhcccCceee---eeeeEEEecCCCCeecccCC
Q psy11813 31 DQTVKTIGLREV---WFFGLQYADSRGDLTWIKLY 62 (70)
Q Consensus 31 d~Vc~~L~L~E~---dYFGL~y~d~~~~~~WLd~~ 62 (70)
..++...+..|+ |.||+.|..+.+.+.||-++
T Consensus 104 ~~i~p~A~w~ERE~~d~fGi~f~ghPdlr~~l~~~ 138 (575)
T PRK11742 104 TKIFPNANWYERETWDMFGITFDGHPHLRRILMPP 138 (575)
T ss_pred hhhcccCCchHHHHHHhcCceeCCCCCCcccCCCC
Confidence 355555666666 59999999999999998764
No 114
>PLN02560 enoyl-CoA reductase
Probab=20.79 E-value=3.3e+02 Score=19.53 Aligned_cols=46 Identities=17% Similarity=0.069 Sum_probs=33.5
Q ss_pred EEEEEEecCC-eE---EEEEcccCchhhhHHHHhcccCceeeeeeeEEEe
Q psy11813 5 MNVRVTTMDA-EL---EFAIQHTTTGKQLFDQTVKTIGLREVWFFGLQYA 50 (70)
Q Consensus 5 ~~~~V~lLD~-~~---~~~v~~~~~G~~L~d~Vc~~L~L~E~dYFGL~y~ 50 (70)
|.+.|....| .+ +++++++++-.+|-.++-+.-+....+=-.|.+.
T Consensus 1 M~I~Vk~~~Gk~i~~~~lev~~~aTV~dLK~~Isk~~~~~~~~RqRL~~~ 50 (308)
T PLN02560 1 MKVTVVSRSGREIIKGGLEVPDSATVADLKKAIHKRKKKYYPSRQRLTLP 50 (308)
T ss_pred CEEEEEcCCCCeecceeEEcCCCCcHHHHHHHHHHHcCCCChhheEEEEe
Confidence 4567777777 55 6899999999999999998877633333467764
No 115
>cd01783 DAGK_delta_RA Ubiquitin-like domain of Diacylgylcerol kinase (DAGK). DAGK_delta_RA Diacylgylcerol kinase (DAGK) phosphorylates the second messenger diacylglycerol to phosphatidic acid as part of a protein kinase C pathway. Nine mammalian DAGK isotypes have been identified, which are classified into five subgroups according to their domain architecture and the DAGK-delta and -theta isozymes, which fall into one such group, contain an RA (Ras-associated) domain. DAGKs also contain a conserved catalytic domain (DAGKc), an assesory domain (DAGKa), and an array of conserved motifs that are likely to play a role in lipid-protein and protein-protein interactions in various DAG/PA-dependent signalling pathways.
Probab=20.66 E-value=1.1e+02 Score=18.55 Aligned_cols=35 Identities=17% Similarity=0.232 Sum_probs=28.9
Q ss_pred EEEEEcccCchhhhHHHHhcccCceeee--eeeEEEe
Q psy11813 16 LEFAIQHTTTGKQLFDQTVKTIGLREVW--FFGLQYA 50 (70)
Q Consensus 16 ~~~~v~~~~~G~~L~d~Vc~~L~L~E~d--YFGL~y~ 50 (70)
+++.|.+.++.+++...+.+++||...+ .|-|.=+
T Consensus 19 ~sv~V~~~tt~~dvv~eaL~kfGl~~~~~~~y~LvEV 55 (97)
T cd01783 19 VSIRVNKDTTVQDVILEVLPLFGLQAECPESFRLIEV 55 (97)
T ss_pred EEEEecccchHHHHHHHHHHHhCcccCCccccEEEEE
Confidence 5688999999999999999999997655 6666543
No 116
>KOG4360|consensus
Probab=20.65 E-value=25 Score=27.58 Aligned_cols=35 Identities=17% Similarity=0.224 Sum_probs=31.1
Q ss_pred HHHHhcccCceeeeeeeEEEecCCCCeecccCCCe
Q psy11813 30 FDQTVKTIGLREVWFFGLQYADSRGDLTWIKLYKK 64 (70)
Q Consensus 30 ~d~Vc~~L~L~E~dYFGL~y~d~~~~~~WLd~~k~ 64 (70)
|..-|++..+.|+-+||-.|..+.+..+|++++-+
T Consensus 504 ~~asc~R~~~dek~fi~k~~e~~~~~tsw~q~a~~ 538 (596)
T KOG4360|consen 504 LRASCRRMISDEKLFIVKPLEGSRTLTSWQQLAQP 538 (596)
T ss_pred HHHHHHhhcCchhhhhcccccccccchHHHHHhhh
Confidence 47789999999999999999999999999987654
Done!