Query psy6184
Match_columns 156
No_of_seqs 122 out of 519
Neff 6.3
Searched_HMMs 46136
Date Fri Aug 16 19:52:14 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6184.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6184hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd03568 VHS_STAM VHS domain fa 100.0 2.4E-38 5.1E-43 241.4 13.7 105 7-111 32-137 (144)
2 cd03569 VHS_Hrs_Vps27p VHS dom 100.0 5E-38 1.1E-42 239.0 13.1 106 6-111 35-141 (142)
3 cd03565 VHS_Tom1 VHS domain fa 100.0 4.1E-37 8.9E-42 233.7 12.6 105 6-110 32-141 (141)
4 cd03567 VHS_GGA VHS domain fam 100.0 1.6E-34 3.5E-39 219.2 12.5 100 6-108 32-137 (139)
5 smart00288 VHS Domain present 100.0 2.2E-33 4.7E-38 211.0 12.3 101 6-106 31-133 (133)
6 PF00790 VHS: VHS domain; Int 100.0 1E-32 2.2E-37 208.5 11.6 100 7-106 37-140 (140)
7 KOG1087|consensus 100.0 6.4E-32 1.4E-36 237.9 12.0 116 6-121 32-152 (470)
8 KOG2199|consensus 100.0 1E-31 2.2E-36 230.1 11.3 132 8-139 41-185 (462)
9 cd03561 VHS VHS domain family; 100.0 2.9E-31 6.2E-36 199.1 12.1 99 6-104 31-133 (133)
10 KOG1818|consensus 99.9 1.8E-24 4E-29 194.8 7.0 130 6-135 39-179 (634)
11 KOG1086|consensus 99.9 2.4E-22 5.1E-27 174.6 10.7 100 6-108 39-144 (594)
12 cd00197 VHS_ENTH_ANTH VHS, ENT 99.8 4.2E-20 9.2E-25 134.6 9.3 79 6-84 31-114 (115)
13 cd03562 CID CID (CTD-Interacti 97.9 3.4E-05 7.4E-10 55.8 5.9 78 9-88 34-111 (114)
14 PF01417 ENTH: ENTH domain; I 97.2 0.0026 5.6E-08 46.8 8.1 74 8-83 35-119 (125)
15 cd03572 ENTH_epsin_related ENT 97.2 0.0029 6.2E-08 47.2 7.8 74 7-82 33-116 (122)
16 smart00582 RPR domain present 96.9 0.0033 7.2E-08 45.5 6.1 76 9-85 29-107 (121)
17 cd03571 ENTH_epsin ENTH domain 96.8 0.012 2.6E-07 43.8 8.4 73 9-83 34-116 (123)
18 KOG2056|consensus 96.3 0.027 5.8E-07 48.6 8.7 76 10-85 55-138 (336)
19 cd03564 ANTH_AP180_CALM ANTH d 95.7 0.039 8.5E-07 40.1 6.1 49 6-54 31-79 (117)
20 smart00273 ENTH Epsin N-termin 95.0 0.076 1.6E-06 39.0 5.7 76 8-83 35-117 (127)
21 PF12348 CLASP_N: CLASP N term 92.6 1.3 2.9E-05 34.7 9.1 75 14-89 133-210 (228)
22 PF04818 CTD_bind: RNA polymer 89.9 1.5 3.3E-05 28.2 5.8 51 30-85 2-59 (64)
23 PF08167 RIX1: rRNA processing 89.3 6.3 0.00014 30.2 9.8 76 9-85 18-97 (165)
24 cd00020 ARM Armadillo/beta-cat 89.2 1.5 3.3E-05 29.9 5.8 69 12-82 49-117 (120)
25 PF13646 HEAT_2: HEAT repeats; 88.9 2.6 5.7E-05 27.7 6.6 56 9-76 28-83 (88)
26 PF13646 HEAT_2: HEAT repeats; 87.8 4.6 0.0001 26.5 7.3 57 14-83 1-58 (88)
27 KOG2160|consensus 86.4 2.8 6E-05 36.5 6.8 68 20-88 132-199 (342)
28 cd00020 ARM Armadillo/beta-cat 83.5 5.7 0.00012 26.9 6.3 73 13-87 8-80 (120)
29 PF11707 Npa1: Ribosome 60S bi 82.0 14 0.0003 31.4 9.2 134 14-154 58-231 (330)
30 KOG2057|consensus 80.5 7.8 0.00017 34.0 7.1 67 13-81 62-139 (499)
31 KOG0251|consensus 79.1 2.8 6.1E-05 38.1 4.2 49 7-55 55-104 (491)
32 KOG1293|consensus 76.7 15 0.00032 34.7 8.1 72 14-86 463-534 (678)
33 smart00229 RasGEFN Guanine nuc 76.1 19 0.00041 25.7 7.2 73 9-81 41-124 (127)
34 cd08319 Death_RAIDD Death doma 76.0 8.4 0.00018 26.7 5.0 70 36-108 5-75 (83)
35 PF01602 Adaptin_N: Adaptin N 75.5 24 0.00052 30.9 9.0 88 10-106 77-165 (526)
36 PF11841 DUF3361: Domain of un 75.2 22 0.00047 27.7 7.6 59 24-84 72-130 (160)
37 KOG2071|consensus 75.0 4.1 9E-05 37.7 4.1 94 7-105 35-137 (579)
38 PF07651 ANTH: ANTH domain; I 74.3 6.7 0.00015 32.1 4.9 47 7-53 34-81 (280)
39 PF12348 CLASP_N: CLASP N term 74.2 14 0.0003 28.9 6.5 70 16-88 57-126 (228)
40 cd08779 Death_PIDD Death Domai 73.9 6.8 0.00015 27.1 4.2 68 37-106 6-74 (86)
41 cd08306 Death_FADD Fas-associa 72.1 9.2 0.0002 26.4 4.5 69 35-107 4-74 (86)
42 PF12783 Sec7_N: Guanine nucle 70.8 43 0.00092 25.3 8.6 64 25-89 35-106 (168)
43 PF02985 HEAT: HEAT repeat; I 70.5 15 0.00033 20.0 4.4 30 14-43 2-31 (31)
44 KOG1077|consensus 70.2 22 0.00048 34.2 7.7 61 10-78 109-170 (938)
45 PF12717 Cnd1: non-SMC mitotic 69.5 41 0.00088 25.8 8.1 68 13-86 26-93 (178)
46 PF11698 V-ATPase_H_C: V-ATPas 68.7 28 0.0006 25.8 6.6 72 11-84 42-114 (119)
47 PF03385 DUF288: Protein of un 67.1 8.6 0.00019 33.9 4.1 86 70-155 70-167 (390)
48 PF00531 Death: Death domain; 66.5 20 0.00044 23.3 5.1 32 72-106 39-71 (83)
49 PTZ00429 beta-adaptin; Provisi 65.7 22 0.00047 34.1 6.9 44 7-50 251-294 (746)
50 PF09324 DUF1981: Domain of un 65.6 13 0.00028 25.6 4.1 35 54-88 16-50 (86)
51 PRK01005 V-type ATP synthase s 63.9 41 0.00089 27.1 7.3 86 26-111 63-165 (207)
52 PF13513 HEAT_EZ: HEAT-like re 62.5 26 0.00057 21.2 4.8 52 26-80 1-52 (55)
53 PF12333 Ipi1_N: Rix1 complex 60.1 58 0.0013 23.0 8.4 52 13-65 12-63 (102)
54 PF08328 ASL_C: Adenylosuccina 59.4 44 0.00095 24.7 6.1 55 10-79 55-109 (115)
55 PF12783 Sec7_N: Guanine nucle 59.3 74 0.0016 23.9 8.8 71 13-85 74-146 (168)
56 PF01602 Adaptin_N: Adaptin N 59.3 58 0.0013 28.5 8.1 85 11-105 113-200 (526)
57 PF06798 PrkA: PrkA serine pro 59.2 15 0.00033 30.4 4.2 55 6-61 35-91 (254)
58 cd01670 Death Death Domain: a 58.5 26 0.00056 22.7 4.5 33 72-107 37-70 (79)
59 smart00005 DEATH DEATH domain, 57.9 16 0.00035 24.4 3.4 36 69-107 42-78 (88)
60 PF14816 FAM178: Family of unk 57.9 1.1E+02 0.0024 27.0 9.4 111 36-146 118-254 (377)
61 PRK09687 putative lyase; Provi 57.3 85 0.0018 26.1 8.3 72 10-81 190-278 (280)
62 cd08317 Death_ank Death domain 55.1 28 0.00061 23.5 4.3 66 37-106 8-75 (84)
63 cd06224 REM Guanine nucleotide 53.7 41 0.00089 23.4 5.2 44 47-90 28-84 (122)
64 smart00549 TAFH TAF homology. 53.4 28 0.00061 24.8 4.1 33 54-86 6-38 (92)
65 smart00229 RasGEFN Guanine nuc 53.3 39 0.00085 24.0 5.0 43 48-90 37-89 (127)
66 cd08777 Death_RIP1 Death Domai 52.2 31 0.00067 23.8 4.2 68 36-106 5-75 (86)
67 PF07531 TAFH: NHR1 homology t 52.2 18 0.0004 25.9 3.0 33 54-86 7-39 (96)
68 PF12755 Vac14_Fab1_bd: Vacuol 52.1 80 0.0017 22.2 7.6 63 11-76 26-88 (97)
69 KOG1105|consensus 52.1 1E+02 0.0023 26.4 8.0 27 63-89 54-80 (296)
70 cd08318 Death_NMPP84 Death dom 52.0 41 0.0009 23.0 4.8 68 36-107 10-78 (86)
71 KOG2374|consensus 51.9 1E+02 0.0022 28.7 8.3 98 12-111 26-151 (661)
72 KOG4535|consensus 51.8 16 0.00034 33.9 3.2 32 12-43 150-181 (728)
73 PF00618 RasGEF_N: RasGEF N-te 51.3 43 0.00093 23.0 4.8 44 47-90 33-90 (104)
74 PF10508 Proteasom_PSMB: Prote 51.2 85 0.0018 28.3 7.9 74 10-85 75-148 (503)
75 PF12830 Nipped-B_C: Sister ch 50.9 1.2E+02 0.0025 23.6 8.2 80 17-104 13-97 (187)
76 KOG1077|consensus 50.9 41 0.00089 32.5 5.8 70 11-84 328-397 (938)
77 cd00183 TFIIS_I N-terminal dom 50.2 59 0.0013 21.7 5.2 23 65-87 53-75 (76)
78 PF04826 Arm_2: Armadillo-like 49.7 1.3E+02 0.0027 24.9 8.1 76 13-90 135-210 (254)
79 cd08805 Death_ank1 Death domai 49.3 42 0.00091 23.2 4.4 67 36-106 7-75 (84)
80 PF08767 CRM1_C: CRM1 C termin 48.7 66 0.0014 27.3 6.4 54 11-64 164-220 (319)
81 cd08804 Death_ank2 Death domai 48.4 39 0.00084 23.2 4.1 66 36-104 7-73 (84)
82 smart00509 TFS2N Domain in the 47.9 82 0.0018 21.0 6.1 22 66-87 52-73 (75)
83 PF14663 RasGEF_N_2: Rapamycin 47.1 69 0.0015 23.1 5.5 29 11-39 7-35 (115)
84 PF07197 DUF1409: Protein of u 46.8 21 0.00046 22.7 2.4 30 36-65 7-37 (51)
85 KOG0915|consensus 45.6 1.2E+02 0.0027 31.7 8.5 83 5-92 1009-1092(1702)
86 KOG0946|consensus 45.1 42 0.00091 32.7 5.0 77 11-88 121-198 (970)
87 PF04826 Arm_2: Armadillo-like 44.0 1.3E+02 0.0028 24.9 7.3 70 14-87 56-126 (254)
88 PLN03200 cellulose synthase-in 43.6 83 0.0018 33.8 7.2 71 13-84 190-260 (2102)
89 PF13812 PPR_3: Pentatricopept 42.7 20 0.00043 18.9 1.6 18 91-108 15-33 (34)
90 PF14852 Fis1_TPR_N: Fis1 N-te 40.9 23 0.0005 20.5 1.8 23 21-43 12-34 (35)
91 smart00543 MIF4G Middle domain 40.0 66 0.0014 24.0 4.7 36 28-64 135-170 (200)
92 PF11841 DUF3361: Domain of un 39.5 1.1E+02 0.0025 23.7 5.9 38 14-51 104-141 (160)
93 KOG2025|consensus 37.2 1.1E+02 0.0023 29.8 6.3 62 14-81 128-189 (892)
94 PF08579 RPM2: Mitochondrial r 36.3 63 0.0014 24.1 3.8 21 91-111 39-60 (120)
95 PF11701 UNC45-central: Myosin 35.4 32 0.00068 26.1 2.2 68 14-81 45-113 (157)
96 PF14500 MMS19_N: Dos2-interac 35.2 2.6E+02 0.0056 23.1 11.6 77 10-88 78-156 (262)
97 PF02631 RecX: RecX family; I 34.4 1.7E+02 0.0037 20.7 8.0 97 10-109 7-109 (121)
98 KOG0132|consensus 34.1 42 0.00091 32.5 3.2 97 11-111 41-145 (894)
99 cd08784 Death_DRs Death Domain 33.4 1.4E+02 0.0029 20.0 4.9 34 72-108 38-72 (79)
100 PTZ00429 beta-adaptin; Provisi 33.4 2.9E+02 0.0063 26.6 8.7 27 10-36 103-129 (746)
101 smart00185 ARM Armadillo/beta- 32.7 85 0.0018 17.1 3.3 27 13-39 13-39 (41)
102 cd08316 Death_FAS_TNFRSF6 Deat 32.1 1.5E+02 0.0033 20.9 5.2 38 69-108 45-82 (97)
103 PF05004 IFRD: Interferon-rela 32.1 2.6E+02 0.0056 23.6 7.5 66 13-78 87-153 (309)
104 cd08803 Death_ank3 Death domai 31.6 1.1E+02 0.0023 21.1 4.2 67 37-106 8-75 (84)
105 PF11707 Npa1: Ribosome 60S bi 31.4 3.2E+02 0.007 23.1 8.0 71 14-84 160-236 (330)
106 COG1413 FOG: HEAT repeat [Ener 31.3 2.9E+02 0.0064 22.7 7.7 65 7-83 69-133 (335)
107 PF08711 Med26: TFIIS helical 30.7 1.1E+02 0.0024 18.6 3.9 20 67-86 32-51 (53)
108 KOG2075|consensus 30.7 1.9E+02 0.004 26.7 6.6 78 10-87 206-296 (521)
109 COG5647 Cullin, a subunit of E 30.5 2.4E+02 0.0052 27.3 7.5 57 15-91 468-525 (773)
110 KOG0151|consensus 30.4 2.1E+02 0.0045 27.8 7.0 81 8-88 462-556 (877)
111 PF10508 Proteasom_PSMB: Prote 29.0 3.8E+02 0.0082 24.1 8.4 67 17-85 165-231 (503)
112 COG5181 HSH155 U2 snRNP splice 28.8 76 0.0016 30.5 3.9 35 12-46 604-641 (975)
113 PF04123 DUF373: Domain of unk 28.1 53 0.0011 28.6 2.6 36 73-108 27-66 (344)
114 TIGR01802 CM_pl-yst monofuncti 28.0 3.4E+02 0.0074 22.7 7.2 25 68-92 183-207 (246)
115 KOG2160|consensus 27.8 4E+02 0.0087 23.3 8.0 78 13-91 167-246 (342)
116 PF11264 ThylakoidFormat: Thyl 27.5 13 0.00027 30.4 -1.2 64 54-119 7-73 (216)
117 PLN02344 chorismate mutase 27.3 3.4E+02 0.0073 23.2 7.2 26 68-93 216-241 (284)
118 PF11882 DUF3402: Domain of un 27.3 90 0.002 27.7 4.0 34 16-49 298-331 (409)
119 PLN03076 ARF guanine nucleotid 27.3 1.9E+02 0.0042 30.7 6.8 58 22-81 1147-1208(1780)
120 cd08315 Death_TRAILR_DR4_DR5 D 27.1 1.6E+02 0.0035 20.6 4.6 33 73-108 47-80 (96)
121 PF02854 MIF4G: MIF4G domain; 26.8 2.6E+02 0.0057 20.6 6.8 55 27-81 142-204 (209)
122 COG5209 RCD1 Uncharacterized p 26.6 1.3E+02 0.0028 25.5 4.5 38 28-65 162-199 (315)
123 cd08324 CARD_NOD1_CARD4 Caspas 25.9 1.7E+02 0.0037 20.5 4.4 26 62-87 37-62 (85)
124 KOG3219|consensus 25.6 1.5E+02 0.0033 23.9 4.7 46 70-118 147-194 (195)
125 PF12993 DUF3877: Domain of un 25.2 61 0.0013 25.7 2.3 40 47-88 87-126 (175)
126 TIGR00756 PPR pentatricopeptid 24.4 64 0.0014 16.5 1.7 18 91-108 14-32 (35)
127 PF08045 CDC14: Cell division 24.3 4.2E+02 0.0092 22.1 7.7 72 13-85 134-207 (257)
128 cd08051 gp6_gp15_like Head-Tai 23.9 2.6E+02 0.0056 19.5 5.2 50 24-86 14-63 (94)
129 TIGR01385 TFSII transcription 23.8 2.3E+02 0.005 24.1 5.7 24 66-89 54-77 (299)
130 PF11698 V-ATPase_H_C: V-ATPas 23.7 1.6E+02 0.0035 21.7 4.2 22 21-42 95-116 (119)
131 PF14726 RTTN_N: Rotatin, an a 23.5 2.8E+02 0.006 19.7 7.6 56 10-65 28-84 (98)
132 PF08951 EntA_Immun: Enterocin 22.9 1.9E+02 0.0041 18.3 4.1 49 54-103 4-54 (75)
133 PF10762 DUF2583: Protein of u 22.8 41 0.00089 23.7 0.8 18 133-154 62-79 (89)
134 PF12074 DUF3554: Domain of un 22.8 3.7E+02 0.0079 22.5 6.8 83 24-107 174-258 (339)
135 COG5096 Vesicle coat complex, 22.4 4.9E+02 0.011 25.3 8.1 63 8-83 88-154 (757)
136 KOG0196|consensus 22.4 1.2E+02 0.0026 29.9 4.0 123 16-154 805-933 (996)
137 PF05804 KAP: Kinesin-associat 22.2 2.1E+02 0.0046 27.4 5.7 71 11-84 289-359 (708)
138 PF01397 Terpene_synth: Terpen 22.1 68 0.0015 25.3 2.0 42 70-111 67-109 (183)
139 COG5369 Uncharacterized conser 22.1 2.1E+02 0.0045 27.1 5.4 72 13-85 474-545 (743)
140 PF09712 PHA_synth_III_E: Poly 21.4 2.6E+02 0.0057 23.6 5.6 89 11-102 190-281 (293)
141 smart00523 DWA Domain A in dwa 21.3 1E+02 0.0022 22.5 2.6 29 9-44 5-33 (109)
142 PF11426 Tn7_TnsC_Int: Tn7 tra 21.3 65 0.0014 20.1 1.4 13 98-110 27-39 (48)
143 PF00514 Arm: Armadillo/beta-c 21.2 1.7E+02 0.0037 16.4 4.2 27 13-39 13-39 (41)
144 KOG0213|consensus 21.1 1.4E+02 0.0031 29.4 4.2 33 13-45 800-835 (1172)
145 KOG2171|consensus 21.0 5.3E+02 0.011 26.2 8.1 71 14-90 350-423 (1075)
146 KOG1820|consensus 20.8 6E+02 0.013 24.9 8.4 87 9-99 368-458 (815)
147 PLN00047 photosystem II biogen 20.1 22 0.00047 30.3 -1.2 63 54-118 63-128 (283)
No 1
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=100.00 E-value=2.4e-38 Score=241.36 Aligned_cols=105 Identities=29% Similarity=0.583 Sum_probs=103.1
Q ss_pred CCChHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHH
Q psy6184 7 TIVPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAHA 86 (156)
Q Consensus 7 ~~~~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~ 86 (156)
+++||+|+++|+|||+|+|||+|++||+|||+||||||.+||.||++++|+++|+++++++++..||+||+++|++|+.+
T Consensus 32 ~~~~k~a~ral~KRl~~~n~~v~l~AL~LLe~~vkNCG~~fh~evask~Fl~eL~kl~~~~~~~~Vk~kil~li~~W~~~ 111 (144)
T cd03568 32 ENGAKDCLKAIMKRLNHKDPNVQLRALTLLDACAENCGKRFHQEVASRDFTQELKKLINDRVHPTVKEKLREVVKQWADE 111 (144)
T ss_pred CccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHhhHHHHHHHHHHhcccCCHHHHHHHHHHHHHHHHH
Confidence 78999999999999999999999999999999999999999999999999999999998879999999999999999999
Q ss_pred hhCCCCCcchH-HHHHhhhCCCCCCC
Q psy6184 87 FRNSPKYRAVP-TKSWMTDKGFKNPS 111 (156)
Q Consensus 87 F~~~~~l~~i~-~Y~~Lk~~Gi~FP~ 111 (156)
|+++|+|++|. +|++|+++||.||.
T Consensus 112 f~~~~~l~~i~~~y~~L~~~G~~f~~ 137 (144)
T cd03568 112 FKNDPSLSLMSDLYKKLKNEGPDLVT 137 (144)
T ss_pred hCCCcccHHHHHHHHHHHHcCCCCCC
Confidence 99999999999 99999999999996
No 2
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=100.00 E-value=5e-38 Score=238.98 Aligned_cols=106 Identities=50% Similarity=0.865 Sum_probs=103.3
Q ss_pred CCCChHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHH
Q psy6184 6 WTIVPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAH 85 (156)
Q Consensus 6 ~~~~~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~ 85 (156)
.+++|+||+++|+|||+++||++|++||+|||+||||||.+||.||++++|+++|++++++.++..||+|++++|+.|+.
T Consensus 35 ~~~~~k~a~ral~krl~~~n~~vql~AL~LLe~~vkNCG~~fh~evas~~fl~~l~~l~~~~~~~~Vk~kil~li~~W~~ 114 (142)
T cd03569 35 KDVQPKYAMRALKKRLLSKNPNVQLYALLLLESCVKNCGTHFHDEVASREFMDELKDLIKTTKNEEVRQKILELIQAWAL 114 (142)
T ss_pred CCCCHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHCCHHHHHHHhhHHHHHHHHHHHcccCCHHHHHHHHHHHHHHHH
Confidence 46799999999999999999999999999999999999999999999999999999999888999999999999999999
Q ss_pred HhhCCCCCcchH-HHHHhhhCCCCCCC
Q psy6184 86 AFRNSPKYRAVP-TKSWMTDKGFKNPS 111 (156)
Q Consensus 86 ~F~~~~~l~~i~-~Y~~Lk~~Gi~FP~ 111 (156)
+|+++|+|+.|. +|++|+++||.||+
T Consensus 115 ~f~~~~~l~~i~~~y~~L~~~G~~FP~ 141 (142)
T cd03569 115 AFRNKPQLKYVVDTYQILKAEGHKFPE 141 (142)
T ss_pred HhCCCcccHHHHHHHHHHHHcCCCCCC
Confidence 999999999999 99999999999995
No 3
>cd03565 VHS_Tom1 VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. The VHS domain of the Tom1 protein is essential for the negative regulation of Interleukin-1 and Tumor Necrosis Factor-induced signaling pathways.
Probab=100.00 E-value=4.1e-37 Score=233.70 Aligned_cols=105 Identities=39% Similarity=0.616 Sum_probs=99.9
Q ss_pred CCCChHHHHHHHHHHhc-CCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHH-HHHhhcc--CCcHHHHHHHHHHHH
Q psy6184 6 WTIVPSHALASIKKKLT-NSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQ-MKELVRG--TQHEEVKAKILELIQ 81 (156)
Q Consensus 6 ~~~~~k~AvraL~KrL~-~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~-l~kl~~~--~~~~~Vk~kil~li~ 81 (156)
.+++||+|+++|+|||+ ++||++|++||+|||+||||||.+||.|||+++|+++ |+++++. .++..||+||+++|+
T Consensus 32 ~~~~~k~a~ralkkRl~~~~n~~v~l~aL~LLe~~vkNCG~~fh~eiask~Fl~e~L~~~i~~~~~~~~~Vk~kil~li~ 111 (141)
T cd03565 32 TEDGPKDAVRALKKRLNGNKNHKEVMLTLTVLETCVKNCGHRFHVLVAKKDFIKDVLVKLINPKNNPPTIVQEKVLALIQ 111 (141)
T ss_pred CCCcHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHccHHHHHHHHHHHhhhHHHHHHHcccCCCcHHHHHHHHHHHH
Confidence 46899999999999998 4799999999999999999999999999999999999 9999964 367899999999999
Q ss_pred HHHHHhhCCCCCcchH-HHHHhhhCCCCCC
Q psy6184 82 AWAHAFRNSPKYRAVP-TKSWMTDKGFKNP 110 (156)
Q Consensus 82 ~Wa~~F~~~~~l~~i~-~Y~~Lk~~Gi~FP 110 (156)
+|+.+|+++|+|++|. +|++|+++||.||
T Consensus 112 ~W~~~f~~~~~l~~i~~~y~~L~~~G~~FP 141 (141)
T cd03565 112 AWADAFRGSPDLTGVVEVYEELKKKGIEFP 141 (141)
T ss_pred HHHHHhCCCccchHHHHHHHHHHHcCCCCC
Confidence 9999999999999999 9999999999999
No 4
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=100.00 E-value=1.6e-34 Score=219.21 Aligned_cols=100 Identities=32% Similarity=0.560 Sum_probs=94.4
Q ss_pred CCCChHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhcc-----CCcHHHHHHHHHHH
Q psy6184 6 WTIVPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRG-----TQHEEVKAKILELI 80 (156)
Q Consensus 6 ~~~~~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~-----~~~~~Vk~kil~li 80 (156)
.+.+|++|+++|+|||+|+||++|++||+|||+||||||.+||.||++++|+++|+++++. .++..||+||+++|
T Consensus 32 ~~~~~k~a~rai~krl~~~n~~v~l~AL~LLe~~vkNCG~~fh~evas~~Fl~el~kl~~~k~~~~~~~~~Vk~kil~li 111 (139)
T cd03567 32 EPEGPQLAVRLLAHKIQSPQEKEALQALTVLEACMKNCGERFHSEVGKFRFLNELIKLVSPKYLGSRTSEKVKTKIIELL 111 (139)
T ss_pred CCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCHHHHHHHHhHHHHHHHHHHhccccCCCCCCHHHHHHHHHHH
Confidence 3579999999999999999999999999999999999999999999999999999999963 47899999999999
Q ss_pred HHHHHHhhCCCCCcchH-HHHHhhhCCCC
Q psy6184 81 QAWAHAFRNSPKYRAVP-TKSWMTDKGFK 108 (156)
Q Consensus 81 ~~Wa~~F~~~~~l~~i~-~Y~~Lk~~Gi~ 108 (156)
+.|+++|+++|+ |. +|++||++|+.
T Consensus 112 ~~W~~~f~~~p~---~~~~Y~~Lk~~G~i 137 (139)
T cd03567 112 YSWTLELPHEPK---IKEAYDMLKKQGII 137 (139)
T ss_pred HHHHHHhcccch---HHHHHHHHHHCCCc
Confidence 999999998888 77 99999999974
No 5
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=100.00 E-value=2.2e-33 Score=210.99 Aligned_cols=101 Identities=41% Similarity=0.707 Sum_probs=96.4
Q ss_pred CCCChHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHH-HHHHHHHHHHHHH
Q psy6184 6 WTIVPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEE-VKAKILELIQAWA 84 (156)
Q Consensus 6 ~~~~~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~-Vk~kil~li~~Wa 84 (156)
.+++|++|+++|+|||+++||++|++||+|||+||+|||.+||.||++++|+++|++++++.++.. |++|++++|+.|+
T Consensus 31 ~~~~~k~a~r~l~krl~~~n~~v~l~AL~lLe~~vkNcg~~f~~ev~s~~fl~~L~~l~~~~~~~~~Vk~kil~li~~W~ 110 (133)
T smart00288 31 TPDGPKDAVRLLKKRLNNKNPHVALLALTLLDACVKNCGSKFHLEVASKEFLNELVKLIKPKYPLPLVKKRILELIQEWA 110 (133)
T ss_pred CCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHhHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHH
Confidence 378999999999999999999999999999999999999999999999999999999998755544 9999999999999
Q ss_pred HHhhCCCCCcchH-HHHHhhhCC
Q psy6184 85 HAFRNSPKYRAVP-TKSWMTDKG 106 (156)
Q Consensus 85 ~~F~~~~~l~~i~-~Y~~Lk~~G 106 (156)
.+|+++|+|+.|. +|+.|+++|
T Consensus 111 ~~f~~~~~~~~i~~~y~~L~~~g 133 (133)
T smart00288 111 DAFKNDPDLSQIVDVYDLLKKKG 133 (133)
T ss_pred HHHcCCCCchHHHHHHHHHHHCc
Confidence 9999999999999 999999998
No 6
>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM. Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....
Probab=100.00 E-value=1e-32 Score=208.50 Aligned_cols=100 Identities=37% Similarity=0.675 Sum_probs=95.3
Q ss_pred CCChHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCc-HH--HHHHHHHHHHHH
Q psy6184 7 TIVPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQH-EE--VKAKILELIQAW 83 (156)
Q Consensus 7 ~~~~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~-~~--Vk~kil~li~~W 83 (156)
+++|++|+++|+|||+|+||++|++||+|||+||+|||.+||.+|++++|+++|.+++++... .. ||+|++++|+.|
T Consensus 37 ~~~~kea~~~l~krl~~~~~~vq~~aL~lld~lvkNcg~~f~~ev~~~~fl~~l~~l~~~~~~~~~~~Vk~k~l~ll~~W 116 (140)
T PF00790_consen 37 PDGAKEAARALRKRLKHGNPNVQLLALTLLDALVKNCGPRFHREVASKEFLDELVKLIKSKKTDPETPVKEKILELLQEW 116 (140)
T ss_dssp TTHHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHSHHHHHHHHTSHHHHHHHHHHHHHTTTHHHSHHHHHHHHHHHHH
T ss_pred CccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHcCCHHHHHHHhHHHHHHHHHHHHccCCCCchhHHHHHHHHHHHHH
Confidence 789999999999999999999999999999999999999999999999999999999976444 43 999999999999
Q ss_pred HHHhhCCCCCcchH-HHHHhhhCC
Q psy6184 84 AHAFRNSPKYRAVP-TKSWMTDKG 106 (156)
Q Consensus 84 a~~F~~~~~l~~i~-~Y~~Lk~~G 106 (156)
+.+|+++|+|+.|. +|++||++|
T Consensus 117 ~~~f~~~~~~~~i~~~y~~Lk~~G 140 (140)
T PF00790_consen 117 AEAFKSDPELSLIQDTYKRLKRKG 140 (140)
T ss_dssp HHHTTTSTTGHHHHHHHHHHHHTT
T ss_pred HHHHCCCCCchHHHHHHHHHHHCc
Confidence 99999999999999 999999998
No 7
>KOG1087|consensus
Probab=99.97 E-value=6.4e-32 Score=237.90 Aligned_cols=116 Identities=31% Similarity=0.468 Sum_probs=107.5
Q ss_pred CCCChHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccC-CcHHHHHHHHHHHHHHH
Q psy6184 6 WTIVPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGT-QHEEVKAKILELIQAWA 84 (156)
Q Consensus 6 ~~~~~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~-~~~~Vk~kil~li~~Wa 84 (156)
.+.+++||+++|+|||++++++||++||+|||+||||||+.||.+|++++|+++|+++++.+ .+.+||+|||.||++|+
T Consensus 32 ~~~~~~eAvralkKRi~~k~s~vq~lALtlLE~cvkNCG~~fh~~Va~k~fL~emVk~~k~~~~~~~Vr~kiL~LI~~W~ 111 (470)
T KOG1087|consen 32 TEGGPKEAVRALKKRLNSKNSKVQLLALTLLETCVKNCGYSFHLQVASKEFLNEMVKRPKNKPRDLKVREKILELIDTWQ 111 (470)
T ss_pred CccCcHHHHHHHHHHhccCCcHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHhccccCCcchhHHHHHHHHHHHHH
Confidence 46789999999999999999999999999999999999999999999999999999999987 89999999999999999
Q ss_pred HHhhC-CCCCcchH-HHHHhhhCCCCCCCC--CCCCCCChh
Q psy6184 85 HAFRN-SPKYRAVP-TKSWMTDKGFKNPSK--SSDSLGLEL 121 (156)
Q Consensus 85 ~~F~~-~~~l~~i~-~Y~~Lk~~Gi~FP~~--~~~a~f~~~ 121 (156)
++|.+ ++.++.+. +|++|+++||+||.+ ++.+.++|+
T Consensus 112 ~af~~~~~~~~~~~~~y~~l~~~G~~FP~r~~~sl~~~~pp 152 (470)
T KOG1087|consen 112 QAFCGPDGYLPDYYQIYDELRRKGVEFPQRDEESLAVLTPP 152 (470)
T ss_pred HHccCCCCcchhHHHHHHHHHHcCCcCCCCccccccccCCC
Confidence 99998 88889999 999999999999995 344455555
No 8
>KOG2199|consensus
Probab=99.97 E-value=1e-31 Score=230.12 Aligned_cols=132 Identities=23% Similarity=0.462 Sum_probs=123.1
Q ss_pred CChHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHHh
Q psy6184 8 IVPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAHAF 87 (156)
Q Consensus 8 ~~~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~F 87 (156)
+++|+++++|.|||.|++|||+|+||+||++||+|||++||+||+|++|.++|.+|+.++++..|++|+..++++|++.|
T Consensus 41 ~~~kd~lk~i~KRln~~dphV~L~AlTLlda~~~NCg~~~r~EVsSr~F~~el~al~~~~~h~kV~~k~~~lv~eWsee~ 120 (462)
T KOG2199|consen 41 DGGKDCLKAIMKRLNHKDPHVVLQALTLLDACVANCGKRFRLEVSSRDFTTELRALIESKAHPKVCEKMRDLVKEWSEEF 120 (462)
T ss_pred cccHHHHHHHHHHhcCCCcchHHHHHHHHHHHHHhcchHHHHHHhhhhHHHHHHHHHhhcccHHHHHHHHHHHHHHHHHh
Confidence 89999999999999999999999999999999999999999999999999999999998899999999999999999999
Q ss_pred hCCCCCcchH-HHHHhhhCCCCCCCC----CCCC--------CCChhhhhhhhhccccccCCccc
Q psy6184 88 RNSPKYRAVP-TKSWMTDKGFKNPSK----SSDS--------LGLELQIFRICHIHFSEIKGIDQ 139 (156)
Q Consensus 88 ~~~~~l~~i~-~Y~~Lk~~Gi~FP~~----~~~a--------~f~~~~~~~~~~~~~~~~~~~~q 139 (156)
++||+|+.|. +|++||++||.|+.. +..+ -.++++++.++++|+.+..++..
T Consensus 121 K~Dp~lsLi~~l~~klk~~g~~f~~~~~k~~k~a~~~~~v~~k~EeEdiaKAi~lSL~E~~~Q~k 185 (462)
T KOG2199|consen 121 KKDPSLSLISALYKKLKEEGITFLVAGSKPEKHAMSTNTVSSKQEEEDIAKAIELSLKEQEKQKK 185 (462)
T ss_pred ccCcchhHHHHHHHHHHHcCCCcccCCCchhHHHhhcccccccccHHHHHHHHHhhHHHHhhchh
Confidence 9999999999 999999999999762 1111 26788999999999999998844
No 9
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=99.97 E-value=2.9e-31 Score=199.12 Aligned_cols=99 Identities=31% Similarity=0.523 Sum_probs=95.0
Q ss_pred CCCChHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhcc--CCcHHHHHHHHHHHHHH
Q psy6184 6 WTIVPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRG--TQHEEVKAKILELIQAW 83 (156)
Q Consensus 6 ~~~~~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~--~~~~~Vk~kil~li~~W 83 (156)
.+++|++|+++|+|||+++||++|++||+|||+||+|||.+||.+|++++|+++|++++.+ .++..||+|++++|+.|
T Consensus 31 ~~~~~k~a~raL~krl~~~n~~vql~AL~lLd~~vkNcg~~f~~~i~s~~fl~~l~~l~~~~~~~~~~Vk~kil~ll~~W 110 (133)
T cd03561 31 KPNGPKEAARAIRKKIKYGNPHVQLLALTLLELLVKNCGKPFHLQVADKEFLLELVKIAKNSPKYDPKVREKALELILAW 110 (133)
T ss_pred CCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCChHHHHHHhhHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHH
Confidence 4789999999999999999999999999999999999999999999999999999999976 68899999999999999
Q ss_pred HHHhhCC-CCCcchH-HHHHhhh
Q psy6184 84 AHAFRNS-PKYRAVP-TKSWMTD 104 (156)
Q Consensus 84 a~~F~~~-~~l~~i~-~Y~~Lk~ 104 (156)
+.+|+++ |++++|. +|+.||+
T Consensus 111 ~~~f~~~~~~~~~~~~~y~~lk~ 133 (133)
T cd03561 111 SESFGGHSEDLPGIEDAYKLLKR 133 (133)
T ss_pred HHHhcCCCccchHHHHHHHHHhC
Confidence 9999988 9999999 9999984
No 10
>KOG1818|consensus
Probab=99.90 E-value=1.8e-24 Score=194.82 Aligned_cols=130 Identities=38% Similarity=0.626 Sum_probs=120.7
Q ss_pred CCCChHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccC-CcHHHHHHHHHHHHHHH
Q psy6184 6 WTIVPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGT-QHEEVKAKILELIQAWA 84 (156)
Q Consensus 6 ~~~~~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~-~~~~Vk~kil~li~~Wa 84 (156)
..+.||++++.|+||++|.|||+++.+|.|+|.||||||..||.|||+++||+.+..++... ++++|+.+++.+++.|+
T Consensus 39 ~~~~~k~slr~~~~~i~h~np~~~~~~~~~~d~cvkn~G~gv~~ei~tre~m~~~~~~l~~~~~~e~v~~~~l~~~q~wa 118 (634)
T KOG1818|consen 39 GGVPPKPSLRGIKKRIDHENPNVQLFTLKLTDHCVKNCGHGVHCEIATREFMDLLKSLLESQRIHEEVKNKILELIQNWA 118 (634)
T ss_pred cCCCCchhHHHHHHHHhccCCCcccchhhhHHHHHhcCCcchhHHHHHHHHHHHHHhhhccccccchHHHHHHHHHHHHH
Confidence 46789999999999999999999999999999999999999999999999999999999765 99999999999999999
Q ss_pred HHhhCCCCCcchH-HHHHhhhCCCCCCC-CCCCCCCChh--------hhhhhhhccccccC
Q psy6184 85 HAFRNSPKYRAVP-TKSWMTDKGFKNPS-KSSDSLGLEL--------QIFRICHIHFSEIK 135 (156)
Q Consensus 85 ~~F~~~~~l~~i~-~Y~~Lk~~Gi~FP~-~~~~a~f~~~--------~~~~~~~~~~~~~~ 135 (156)
.+|++.+.|.++. +|+.|+.+|+.||+ ++.|+||+.+ +-|..|+..|...+
T Consensus 119 ~af~~~~~~~~v~~t~~~lk~~g~~Fpe~~e~d~mf~~~~~pdW~D~~~C~rCr~~F~~~~ 179 (634)
T KOG1818|consen 119 AAFRNSSKYSYVLDTYQKLKGGGHVFPELDENDAMFDAETAPDWIDSEECLRCRVKFGLTN 179 (634)
T ss_pred HHccCchHHHHHHHHHHHHhcCCccccccccchhhhcccCCcccccccccceeeeeeeecc
Confidence 9999999999999 99999999999999 6777787554 46888888888776
No 11
>KOG1086|consensus
Probab=99.88 E-value=2.4e-22 Score=174.59 Aligned_cols=100 Identities=31% Similarity=0.533 Sum_probs=94.5
Q ss_pred CCCChHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhcc-----CCcHHHHHHHHHHH
Q psy6184 6 WTIVPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRG-----TQHEEVKAKILELI 80 (156)
Q Consensus 6 ~~~~~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~-----~~~~~Vk~kil~li 80 (156)
...||-.|++.|.++|+++...++++||++||+||+|||++||.|+++.+|+|+|+++++. .+..+||.||++++
T Consensus 39 dp~gp~lAv~LlaHKiqSPqe~EAl~altvLe~cmkncGekfH~evgkfrFLNELIkvvsPKYlG~~tSekvKtkiIelL 118 (594)
T KOG1086|consen 39 DPEGPLLAVRLLAHKIQSPQEWEALQALTVLEYCMKNCGEKFHEEVGKFRFLNELIKVVSPKYLGSRTSEKVKTKIIELL 118 (594)
T ss_pred CCCCchhHHHHHHhhcCChhHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhCchhcchhhhHHHHHHHHHHH
Confidence 3568999999999999999999999999999999999999999999999999999999974 47899999999999
Q ss_pred HHHHHHhhCCCCCcchH-HHHHhhhCCCC
Q psy6184 81 QAWAHAFRNSPKYRAVP-TKSWMTDKGFK 108 (156)
Q Consensus 81 ~~Wa~~F~~~~~l~~i~-~Y~~Lk~~Gi~ 108 (156)
..|..+|+.+++ |+ +|++||++||.
T Consensus 119 fsWtv~lpe~~K---ikdaYqmLKkqgIi 144 (594)
T KOG1086|consen 119 FSWTVSLPEEPK---IKDAYQMLKKQGII 144 (594)
T ss_pred hhheecCcccch---HHHHHHHHHhcCcc
Confidence 999999999999 77 99999999985
No 12
>cd00197 VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membra
Probab=99.82 E-value=4.2e-20 Score=134.57 Aligned_cols=79 Identities=41% Similarity=0.718 Sum_probs=72.5
Q ss_pred CCCChHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhh-----ccCCcHHHHHHHHHHH
Q psy6184 6 WTIVPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELV-----RGTQHEEVKAKILELI 80 (156)
Q Consensus 6 ~~~~~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~-----~~~~~~~Vk~kil~li 80 (156)
.+.++++++++|+|||+++||++++.||+|||+||||||++||.+|+++.|+.++.+.. ....+..||+++++++
T Consensus 31 ~~~~~~~~~~~l~kRl~~~~~~~~lkaL~lLe~lvkN~g~~f~~~i~~~~~~~~l~~~~~~~~~~~~~~~~Vr~k~~~l~ 110 (115)
T cd00197 31 TNVGPKEAVDAIKKRINNKNPHVVLKALTLLEYCVKNCGERFHQEVASNDFAVELLKFDKSKLLGDDVSTNVREKAIELV 110 (115)
T ss_pred CCccHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHccHHHHHHHHHhHHHHHHHHhhccccccCCCChHHHHHHHHHH
Confidence 35789999999999999999999999999999999999999999999999999997742 2346899999999999
Q ss_pred HHHH
Q psy6184 81 QAWA 84 (156)
Q Consensus 81 ~~Wa 84 (156)
+.|+
T Consensus 111 ~~w~ 114 (115)
T cd00197 111 QLWA 114 (115)
T ss_pred HHHh
Confidence 9997
No 13
>cd03562 CID CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1. Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.
Probab=97.89 E-value=3.4e-05 Score=55.75 Aligned_cols=78 Identities=21% Similarity=0.330 Sum_probs=61.5
Q ss_pred ChHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHHhh
Q psy6184 9 VPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAHAFR 88 (156)
Q Consensus 9 ~~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~F~ 88 (156)
.+++.+..+.++|+...|..-+.+|.|+|.+++|||.+-...+.. .+.+-+..... ..+..+|.++..++..|.+.+.
T Consensus 34 ~a~~iv~~i~~~i~~~~~~~KL~~LYL~dsIvkn~~~~~~~~~~~-~~~~~f~~~~~-~~~~~~r~kl~rl~~iW~~~~~ 111 (114)
T cd03562 34 HAKEIVEIIEKHIKKCPPEQKLPLLYLLDSIVKNVGRKYKEFFSE-FLVPLFLDAYE-KVDEKTRKKLERLLNIWEERFV 111 (114)
T ss_pred HHHHHHHHHHHHHHhCCcccchHHHHHHHHHHHHcccchHHHHHH-HHHHHHHHHHH-hCCHHHHHHHHHHHHHccCCCC
Confidence 467889999999999999999999999999999999996654332 22333333333 6789999999999999987653
No 14
>PF01417 ENTH: ENTH domain; InterPro: IPR001026 The ENTH (Epsin N-terminal homology) domain is approximately 150 amino acids in length and is always found located at the N-termini of proteins. The domain forms a compact globular structure, composed of 9 alpha-helices connected by loops of varying length. The general topology is determined by three helical hairpins that are stacked consecutively with a right hand twist []. An N-terminal helix folds back, forming a deep basic groove that forms the binding pocket for the Ins(1,4,5)P3 ligand []. The ligand is coordinated by residues from surrounding alpha-helices and all three phosphates are multiply coordinated. The coordination of Ins(1,4,5)P3 suggests that ENTH is specific for particular head groups. Proteins containing this domain have been found to bind PtdIns(4,5)P2 and PtdIns(1,4,5)P3 suggesting that the domain may be a membrane interacting module. The main function of proteins containing this domain appears to be to act as accessory clathrin adaptors in endocytosis, Epsin is able to recruit and promote clathrin polymerisation on a lipid monolayer, but may have additional roles in signalling and actin regulation []. Epsin causes a strong degree of membrane curvature and tubulation, even fragmentation of membranes with a high PtdIns(4,5)P2 content. Epsin binding to membranes facilitates their deformation by insertion of the N-terminal helix into the outer leaflet of the bilayer, pushing the head groups apart. This would reduce the energy needed to curve the membrane into a vesicle, making it easier for the clathrin cage to fix and stabilise the curved membrane. This points to a pioneering role for epsin in vesicle budding as it provides both a driving force and a link between membrane invagination and clathrin polymerisation. ; PDB: 1H0A_A 1EYH_A 1EDU_A 2QY7_B 1XGW_A 2V8S_E 1VDY_A 2DCP_A 1INZ_A 3ONL_B ....
Probab=97.21 E-value=0.0026 Score=46.81 Aligned_cols=74 Identities=24% Similarity=0.280 Sum_probs=55.4
Q ss_pred CChHHHHHHHHHHh---cCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhc-----cC---CcHHHHHHH
Q psy6184 8 IVPSHALASIKKKL---TNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVR-----GT---QHEEVKAKI 76 (156)
Q Consensus 8 ~~~k~AvraL~KrL---~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~-----~~---~~~~Vk~ki 76 (156)
....+.+..|.||| ..+++++++-||.||+.|++||...|-.++ ++-...|..+.. .. ....||+++
T Consensus 35 ~~~~~I~~~l~kRL~~~~~k~wr~~~KaL~ll~yLl~nG~~~~~~~~--~~~~~~I~~l~~f~~~d~~g~d~~~~VR~~A 112 (125)
T PF01417_consen 35 KDCQEIMDVLWKRLSKSDGKNWRHVYKALTLLEYLLKNGSERFVDEL--RDHIDIIRELQDFQYVDPKGKDQGQNVREKA 112 (125)
T ss_dssp HHHHHHHHHHHHHHHSSTSSGHHHHHHHHHHHHHHHHHS-HHHHHHH--HHTHHHHHGGGG---BBTTSTBHHHHHHHHH
T ss_pred ccHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHHHHHHCCHHHHHHH--HHHHHHHhhcceeeccCCCCccHHHHHHHHH
Confidence 45678899999999 789999999999999999999999999888 444455555432 11 124588888
Q ss_pred HHHHHHH
Q psy6184 77 LELIQAW 83 (156)
Q Consensus 77 l~li~~W 83 (156)
-+++...
T Consensus 113 ~~i~~lL 119 (125)
T PF01417_consen 113 KEILELL 119 (125)
T ss_dssp HHHHHHH
T ss_pred HHHHHHh
Confidence 8777643
No 15
>cd03572 ENTH_epsin_related ENTH domain, Epsin Related family; composed of hypothetical proteins containing an ENTH-like domain. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. ENTH and ANTH (E/ANTH) domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. E/ANTH domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the t
Probab=97.15 E-value=0.0029 Score=47.24 Aligned_cols=74 Identities=24% Similarity=0.347 Sum_probs=56.5
Q ss_pred CCChHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhc--c--------CCcHHHHHHH
Q psy6184 7 TIVPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVR--G--------TQHEEVKAKI 76 (156)
Q Consensus 7 ~~~~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~--~--------~~~~~Vk~ki 76 (156)
.....+.+..|-|||++++|+|-+-||.+|+.|+.+++..|.+++... ...+..+.. . .....||..+
T Consensus 33 ~~~~~ei~d~L~kRL~~~~~hVK~K~Lrilk~l~~~G~~~f~~~~~~~--~~~Ik~~~~f~g~~Dp~~Gd~~~~~VR~~A 110 (122)
T cd03572 33 VGSCQELLEYLLKRLKRSSPHVKLKVLKIIKHLCEKGNSDFKRELQRN--SAQIRECANYKGPPDPLKGDSLNEKVREEA 110 (122)
T ss_pred HHHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHHhhCCHHHHHHHHHh--HHHHHHHHHcCCCCCcccCcchhHHHHHHH
Confidence 355778999999999999999999999999999999999999987544 233333322 1 2346788877
Q ss_pred HHHHHH
Q psy6184 77 LELIQA 82 (156)
Q Consensus 77 l~li~~ 82 (156)
.+++..
T Consensus 111 ~El~~~ 116 (122)
T cd03572 111 QELIKA 116 (122)
T ss_pred HHHHHH
Confidence 777654
No 16
>smart00582 RPR domain present in proteins, which are involved in regulation of nuclear pre-mRNA.
Probab=96.89 E-value=0.0033 Score=45.51 Aligned_cols=76 Identities=22% Similarity=0.338 Sum_probs=55.2
Q ss_pred ChHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhc---cCCcHHHHHHHHHHHHHHHH
Q psy6184 9 VPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVR---GTQHEEVKAKILELIQAWAH 85 (156)
Q Consensus 9 ~~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~---~~~~~~Vk~kil~li~~Wa~ 85 (156)
.+++.+..|.+.+....+..-+..|.|++.+++||+.+.-..+ ...|...+...+. ...+.++++++..++..|.+
T Consensus 29 ~a~~Iv~~i~~~~~~~~~~~kL~~LYlindIl~n~~~~~~~~f-~~~~~~~~~~~~~~~~~~~~~~~~~ki~kll~iW~~ 107 (121)
T smart00582 29 HAKEIVELWEKYIKKAPPPRKLPLLYLLDSIVQNSKRKYGSEF-GDELGPVFQDALRDVLGAANDETKKKIRRLLNIWEE 107 (121)
T ss_pred HHHHHHHHHHHHHHhCCccceehhHHhHHHHHHHHhhccHHHH-HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhc
Confidence 4578899999999877777888999999999999987632111 1233333333322 23457899999999999997
No 17
>cd03571 ENTH_epsin ENTH domain, Epsin family; The epsin (Eps15 interactor) N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. ENTH and ANTH (E/ANTH) domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. E/ANTH domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that E/ANTH domains are univ
Probab=96.78 E-value=0.012 Score=43.81 Aligned_cols=73 Identities=22% Similarity=0.238 Sum_probs=53.9
Q ss_pred ChHHHHHHHHHHhcC--CCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhh-----cc---CCcHHHHHHHHH
Q psy6184 9 VPSHALASIKKKLTN--SNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELV-----RG---TQHEEVKAKILE 78 (156)
Q Consensus 9 ~~k~AvraL~KrL~~--~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~-----~~---~~~~~Vk~kil~ 78 (156)
...+.+..|.|||.. +|...++-||+|||.|++|+.+.|-.++.+. +..|..|- .. .....||+|+-.
T Consensus 34 ~~~~Im~~l~kRL~~~~k~WR~vyKaL~lleyLl~nGse~vv~~~r~~--~~~i~~L~~F~~~d~~g~d~G~~VR~ka~~ 111 (123)
T cd03571 34 EFQEIMSMLWKRLNDKGKNWRHVYKALTLLEYLLKNGSERVVDDAREN--LYIIRTLKDFQYIDENGKDQGINVREKAKE 111 (123)
T ss_pred HHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHhCCHHHHHHHHHh--HHHHHhhccceeeCCCCCchhHHHHHHHHH
Confidence 446889999999964 6999999999999999999999988877433 33333332 11 133778988888
Q ss_pred HHHHH
Q psy6184 79 LIQAW 83 (156)
Q Consensus 79 li~~W 83 (156)
++...
T Consensus 112 i~~Ll 116 (123)
T cd03571 112 ILELL 116 (123)
T ss_pred HHHHh
Confidence 77654
No 18
>KOG2056|consensus
Probab=96.32 E-value=0.027 Score=48.65 Aligned_cols=76 Identities=22% Similarity=0.207 Sum_probs=55.9
Q ss_pred hHHHHHHHHHHhc--CCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHh---hcc---CCcHHHHHHHHHHHH
Q psy6184 10 PSHALASIKKKLT--NSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKEL---VRG---TQHEEVKAKILELIQ 81 (156)
Q Consensus 10 ~k~AvraL~KrL~--~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl---~~~---~~~~~Vk~kil~li~ 81 (156)
..+.|-.|.||+. .+|...++-||+|||.|++|+.++|-.++-..-++-++.+= +.. .....||+|+-+++.
T Consensus 55 ~~eIm~vi~kRl~d~gknWR~VyKaLtlleyLl~~GSErv~~~~ren~~~I~tL~~Fq~iD~~G~dqG~nVRkkak~l~~ 134 (336)
T KOG2056|consen 55 YQEIMDVLWKRLNDSGKNWRHVYKALTLLEYLLKNGSERVVDETRENIYTIETLKDFQYIDEDGKDQGLNVRKKAKELLS 134 (336)
T ss_pred HHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHhcCcHHHHHHHHhhhHHHHHHhhceeeCCCCccchHHHHHHHHHHHH
Confidence 4678889999995 58999999999999999999999887776544444443322 121 133678888888877
Q ss_pred HHHH
Q psy6184 82 AWAH 85 (156)
Q Consensus 82 ~Wa~ 85 (156)
...+
T Consensus 135 LL~D 138 (336)
T KOG2056|consen 135 LLED 138 (336)
T ss_pred Hhcc
Confidence 6654
No 19
>cd03564 ANTH_AP180_CALM ANTH domain family; composed of adaptor protein 180 (AP180), clathrin assembly lymphoid myeloid leukemia protein (CALM) and similar proteins. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. AP180 and CALM play important roles in clathrin-mediated endocytosis. AP180 is a brain-specific clathrin-binding protein which stimulates clathrin assembly during the recycling of synaptic vesicles. The ANTH domain is structurally similar to the VHS domain and is composed of a superhelix of eight alpha helices. ANTH domains bind both inositol phospholipids and proteins, and contribute to the nucleation and formation of clathrin coats on membranes. ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that the ANTH domain is a universal component of the machine
Probab=95.69 E-value=0.039 Score=40.10 Aligned_cols=49 Identities=16% Similarity=0.188 Sum_probs=44.1
Q ss_pred CCCChHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccH
Q psy6184 6 WTIVPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTK 54 (156)
Q Consensus 6 ~~~~~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask 54 (156)
++.+..+.+.+|.+|+..+|+-+++-||.||.-+++++.+.|..++.+.
T Consensus 31 ~~~~~~~~~~~l~~Rl~~~~w~v~~K~LillH~llr~G~~~~~~~~~~~ 79 (117)
T cd03564 31 SPASIPSFASALSRRLLDRNWVVVLKALILLHRLLREGHPSFLQELLSR 79 (117)
T ss_pred CCCCHHHHHHHHHHHHccCcHHHHHHHHHHHHHHHhcCCHHHHHHHHHc
Confidence 3678999999999999889999999999999999999999988876553
No 20
>smart00273 ENTH Epsin N-terminal homology (ENTH) domain.
Probab=94.99 E-value=0.076 Score=38.99 Aligned_cols=76 Identities=14% Similarity=0.169 Sum_probs=52.5
Q ss_pred CChHHHHHHHHHHhcCC-CHHHHHHHHHHHHHHHHccchhHHhhhccHH-HHHHHHHhhc-c----CCcHHHHHHHHHHH
Q psy6184 8 IVPSHALASIKKKLTNS-NPHIVLYALLVLESCVKNCGNLIHDEVGTKA-FMEQMKELVR-G----TQHEEVKAKILELI 80 (156)
Q Consensus 8 ~~~k~AvraL~KrL~~~-n~~v~l~AL~LLe~~vkNCG~~fh~eIask~-Fl~~l~kl~~-~----~~~~~Vk~kil~li 80 (156)
....+.+.+|.+||... |+.+++-||.||+.|++|+.+.+-.++.+.. .+..|...-. + ....-|+.+...+.
T Consensus 35 ~~~~~i~~~l~~Rl~~~~~w~~v~KsL~llh~ll~~G~~~~~~~~~~~~~~i~~L~~f~~~~~~~~d~g~~VR~ya~~L~ 114 (127)
T smart00273 35 SSFAEIMAVLWRRLNDTKNWRVVYKALILLHYLLRNGSPRVILEALRNRNRILNLSDFQDIDSRGKDQGANIRTYAKYLL 114 (127)
T ss_pred hhHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHhcCCHHHHHHHHHhhHHHhhHhhCeecCCCCeeCcHHHHHHHHHHH
Confidence 56789999999999755 9999999999999999999987765553322 2222333221 1 12356777777766
Q ss_pred HHH
Q psy6184 81 QAW 83 (156)
Q Consensus 81 ~~W 83 (156)
..-
T Consensus 115 ~~l 117 (127)
T smart00273 115 ERL 117 (127)
T ss_pred HHH
Confidence 543
No 21
>PF12348 CLASP_N: CLASP N terminal; InterPro: IPR024395 This domain is found in the N-terminal region of CLIP-associated proteins (CLASPs), which are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules [, ]. The domain is also found in other proteins involved in microtubule binding, including STU1, MOR1 and spindle pole body component Alp14.; PDB: 2QK2_A.
Probab=92.56 E-value=1.3 Score=34.74 Aligned_cols=75 Identities=17% Similarity=0.240 Sum_probs=50.1
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHHccc---hhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHHhhC
Q psy6184 14 LASIKKKLTNSNPHIVLYALLVLESCVKNCG---NLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAHAFRN 89 (156)
Q Consensus 14 vraL~KrL~~~n~~v~l~AL~LLe~~vkNCG---~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~F~~ 89 (156)
...+..-++++||.+-..++..+..++.+.| ..+.....-+.+...+.+.+.+ .+.+||+-...++......|+.
T Consensus 133 ~~~l~~~~~~Kn~~vR~~~~~~l~~~l~~~~~~~~~l~~~~~~~~l~~~l~~~l~D-~~~~VR~~Ar~~~~~l~~~~~~ 210 (228)
T PF12348_consen 133 LEILSQGLKSKNPQVREECAEWLAIILEKWGSDSSVLQKSAFLKQLVKALVKLLSD-ADPEVREAARECLWALYSHFPE 210 (228)
T ss_dssp HHHHHHHTT-S-HHHHHHHHHHHHHHHTT-----GGG--HHHHHHHHHHHHHHHTS-S-HHHHHHHHHHHHHHHHHH-H
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHHHHccchHhhhcccchHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHHCCH
Confidence 6677777789999999999999999999999 3333322224445555555554 5788999999999888888764
No 22
>PF04818 CTD_bind: RNA polymerase II-binding domain.; InterPro: IPR006903 This entry represents a conserved region found in a number of uncharacterised eukaryotic proteins.; PDB: 2L0I_A 2KM4_A 3D9I_B 3D9N_B 3D9O_A 3D9P_B 3D9K_A 3D9M_A 3D9J_A 3D9L_A ....
Probab=89.89 E-value=1.5 Score=28.21 Aligned_cols=51 Identities=18% Similarity=0.345 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHccchhHHhhhccHHHHHHHH----Hhhc---cCCcHHHHHHHHHHHHHHHH
Q psy6184 30 LYALLVLESCVKNCGNLIHDEVGTKAFMEQMK----ELVR---GTQHEEVKAKILELIQAWAH 85 (156)
Q Consensus 30 l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~----kl~~---~~~~~~Vk~kil~li~~Wa~ 85 (156)
+.-|.|++..++||... ...+|.+.+. .++. ...+.++++++..++..|.+
T Consensus 2 L~~lYl~ndI~q~sk~k-----~~~~f~~~F~~~l~~~~~~~~~~~~~~~~~kv~rll~iW~~ 59 (64)
T PF04818_consen 2 LALLYLANDILQNSKRK-----NPDEFAPAFSPVLPDAFAHAYKNVDPEVRKKVQRLLNIWEE 59 (64)
T ss_dssp HHHHHHHHHHHHHHHHH-----TTHCHHHHHHCCHHHHHHHHCCCS-HHHHHHHHHHHHHHHH
T ss_pred cceeehHHHHHHHhhhc-----ChHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhC
Confidence 34578999999999654 2334444433 3332 34589999999999999986
No 23
>PF08167 RIX1: rRNA processing/ribosome biogenesis
Probab=89.27 E-value=6.3 Score=30.20 Aligned_cols=76 Identities=11% Similarity=0.125 Sum_probs=55.3
Q ss_pred ChHHHHHHHHHHh----cCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHH
Q psy6184 9 VPSHALASIKKKL----TNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWA 84 (156)
Q Consensus 9 ~~k~AvraL~KrL----~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa 84 (156)
..+.++..+..|| +++++..-..++.|+.+.+.+||...-.+- ...++..+.+++++..+..+++-+...+..--
T Consensus 18 ~~~~~l~~l~~ri~~LL~s~~~~~rw~G~~Ll~~~~~~~~~e~l~~~-~~~W~~~Ll~~L~~~~~~~~~~~ai~~L~~l~ 96 (165)
T PF08167_consen 18 PSKSALHKLVTRINSLLQSKSAYSRWAGLCLLKVTVEQCSWEILLSH-GSQWLRALLSILEKPDPPSVLEAAIITLTRLF 96 (165)
T ss_pred cCHHHHHHHHHHHHHHhCCCChhhHHHHHHHHHHHHHHhhHHHHHHH-HHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHH
Confidence 3577777777776 468899999999999999999965543322 37899999999987666666665554444433
Q ss_pred H
Q psy6184 85 H 85 (156)
Q Consensus 85 ~ 85 (156)
.
T Consensus 97 ~ 97 (165)
T PF08167_consen 97 D 97 (165)
T ss_pred H
Confidence 3
No 24
>cd00020 ARM Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
Probab=89.20 E-value=1.5 Score=29.93 Aligned_cols=69 Identities=13% Similarity=0.148 Sum_probs=53.2
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHH
Q psy6184 12 HALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQA 82 (156)
Q Consensus 12 ~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~ 82 (156)
+++..|.+-|.+.|+.++..|+..|-.+..++... ...+....++..+.+++... +.++++.++..+..
T Consensus 49 ~~i~~l~~~l~~~~~~v~~~a~~~L~~l~~~~~~~-~~~~~~~g~l~~l~~~l~~~-~~~~~~~a~~~l~~ 117 (120)
T cd00020 49 GGLPALVQLLKSEDEEVVKAALWALRNLAAGPEDN-KLIVLEAGGVPKLVNLLDSS-NEDIQKNATGALSN 117 (120)
T ss_pred CChHHHHHHHhCCCHHHHHHHHHHHHHHccCcHHH-HHHHHHCCChHHHHHHHhcC-CHHHHHHHHHHHHH
Confidence 45667777788899999999999999999987643 33334456788888888754 67888888877754
No 25
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=88.85 E-value=2.6 Score=27.69 Aligned_cols=56 Identities=16% Similarity=0.232 Sum_probs=27.2
Q ss_pred ChHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHH
Q psy6184 9 VPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKI 76 (156)
Q Consensus 9 ~~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~ki 76 (156)
+..+++..|..-++++|+.|...|+.-|..+ ++++.+..|.+++.+..+..|+..+
T Consensus 28 ~~~~~~~~L~~~l~d~~~~vr~~a~~aL~~i------------~~~~~~~~L~~~l~~~~~~~vr~~a 83 (88)
T PF13646_consen 28 GDPEAIPALIELLKDEDPMVRRAAARALGRI------------GDPEAIPALIKLLQDDDDEVVREAA 83 (88)
T ss_dssp THHHHHHHHHHHHTSSSHHHHHHHHHHHHCC------------HHHHTHHHHHHHHTC-SSHHHHHHH
T ss_pred CCHhHHHHHHHHHcCCCHHHHHHHHHHHHHh------------CCHHHHHHHHHHHcCCCcHHHHHHH
Confidence 3445555555555555555555555544422 2344455555555443344444433
No 26
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=87.81 E-value=4.6 Score=26.47 Aligned_cols=57 Identities=16% Similarity=0.276 Sum_probs=44.6
Q ss_pred HHHHHHHh-cCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHH
Q psy6184 14 LASIKKKL-TNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAW 83 (156)
Q Consensus 14 vraL~KrL-~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~W 83 (156)
+..|.+.| +++++.+...|+.+|. ++.+.+.+..|..++++ .+..||..+...+..-
T Consensus 1 i~~L~~~l~~~~~~~vr~~a~~~L~------------~~~~~~~~~~L~~~l~d-~~~~vr~~a~~aL~~i 58 (88)
T PF13646_consen 1 IPALLQLLQNDPDPQVRAEAARALG------------ELGDPEAIPALIELLKD-EDPMVRRAAARALGRI 58 (88)
T ss_dssp HHHHHHHHHTSSSHHHHHHHHHHHH------------CCTHHHHHHHHHHHHTS-SSHHHHHHHHHHHHCC
T ss_pred CHHHHHHHhcCCCHHHHHHHHHHHH------------HcCCHhHHHHHHHHHcC-CCHHHHHHHHHHHHHh
Confidence 35678888 8999999999998887 44566889999998854 6778998887776543
No 27
>KOG2160|consensus
Probab=86.41 E-value=2.8 Score=36.51 Aligned_cols=68 Identities=18% Similarity=0.213 Sum_probs=58.8
Q ss_pred HhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHHhh
Q psy6184 20 KLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAHAFR 88 (156)
Q Consensus 20 rL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~F~ 88 (156)
-+++.++.+--+|..++-+|+.|-... +.+|-...|+..|.++++...+..+|.|+|--|...=..|+
T Consensus 132 ~l~~~~~~lR~~Aa~Vigt~~qNNP~~-Qe~v~E~~~L~~Ll~~ls~~~~~~~r~kaL~AissLIRn~~ 199 (342)
T KOG2160|consen 132 YLENSDAELRELAARVIGTAVQNNPKS-QEQVIELGALSKLLKILSSDDPNTVRTKALFAISSLIRNNK 199 (342)
T ss_pred HhcCCcHHHHHHHHHHHHHHHhcCHHH-HHHHHHcccHHHHHHHHccCCCchHHHHHHHHHHHHHhcCc
Confidence 778999999999999999999997554 77777778999999999888888999999988887766554
No 28
>cd00020 ARM Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
Probab=83.49 E-value=5.7 Score=26.94 Aligned_cols=73 Identities=16% Similarity=0.144 Sum_probs=57.2
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHHh
Q psy6184 13 ALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAHAF 87 (156)
Q Consensus 13 AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~F 87 (156)
.+..|.+-|.+.++.+...|+..|..+..+.... ...+.+.+.++.+.+++.+ .+..|+...+..+...+...
T Consensus 8 ~i~~l~~~l~~~~~~~~~~a~~~l~~l~~~~~~~-~~~~~~~~~i~~l~~~l~~-~~~~v~~~a~~~L~~l~~~~ 80 (120)
T cd00020 8 GLPALVSLLSSSDENVQREAAWALSNLSAGNNDN-IQAVVEAGGLPALVQLLKS-EDEEVVKAALWALRNLAAGP 80 (120)
T ss_pred ChHHHHHHHHcCCHHHHHHHHHHHHHHhcCCHHH-HHHHHHCCChHHHHHHHhC-CCHHHHHHHHHHHHHHccCc
Confidence 5777888889999999999999999998875333 3334445888888888876 47789999999998887553
No 29
>PF11707 Npa1: Ribosome 60S biogenesis N-terminal; InterPro: IPR021714 Npa1p is required for ribosome biogenesis and operates in the same functional environment as Rsa3p and Dbp6p during early maturation of 60S ribosomal subunits []. The protein partners of Npa1p include eight putative helicases as well as the novel Npa2p factor. Npa1p can also associate with a subset of H/ACA and C/D small nucleolar RNPs (snoRNPs) involved in the chemical modification of residues in the vicinity of the peptidyl transferase centre []. The protein has also been referred to as Urb1, and this domain at the N-terminal is one of several conserved regions along the length.
Probab=82.01 E-value=14 Score=31.43 Aligned_cols=134 Identities=22% Similarity=0.281 Sum_probs=82.3
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHH-ccchhHHhhhccHHHHH-HHHHhhcc-------------------------
Q psy6184 14 LASIKKKLTNSNPHIVLYALLVLESCVK-NCGNLIHDEVGTKAFME-QMKELVRG------------------------- 66 (156)
Q Consensus 14 vraL~KrL~~~n~~v~l~AL~LLe~~vk-NCG~~fh~eIask~Fl~-~l~kl~~~------------------------- 66 (156)
++.|-+-|.+..+..+.-+|.||-++|. |.|..-..-+...+|-. .+.+++..
T Consensus 58 ~k~lyr~L~~~~~~~~~~~LrLL~~iv~f~~g~~a~~v~~~fd~~~~~l~kll~~~~~~~~~~~~~~~~~~siR~~fI~F 137 (330)
T PF11707_consen 58 LKLLYRSLSSSKPSLTNPALRLLTAIVSFDGGALAREVLRSFDFSLKSLPKLLTPRKKEKEKDSESSKSKPSIRTNFIRF 137 (330)
T ss_pred HHHHHHHhCcCcHHHHHHHHHHHHHHHccCCHHHHHHHHHhcCCchhhHHHHhccccccccccccccccCcCHHHHHHHH
Confidence 5667777777889999999999999999 88887776666677764 35566531
Q ss_pred ------CCcHHHHHHHHHH---HHHHHHHhhCCCCCcchH-HHHHhhhCCC---CCCCCCCCCCCChhhhhhhhhccccc
Q psy6184 67 ------TQHEEVKAKILEL---IQAWAHAFRNSPKYRAVP-TKSWMTDKGF---KNPSKSSDSLGLELQIFRICHIHFSE 133 (156)
Q Consensus 67 ------~~~~~Vk~kil~l---i~~Wa~~F~~~~~l~~i~-~Y~~Lk~~Gi---~FP~~~~~a~f~~~~~~~~~~~~~~~ 133 (156)
..+..++..+|+. +..|-.....||. ..|. +-+-|+..=+ .||..---.+|.+..+.++.. +|.
T Consensus 138 ~Lsfl~~~~~~~~~~lL~~~~~~~~l~k~l~~D~~-~~v~~iL~~l~~~Vl~~~~v~r~~K~~~fn~~~L~~l~~--Ly~ 214 (330)
T PF11707_consen 138 WLSFLSSGDPELKRDLLSQKKLMSALFKGLRKDPP-ETVILILETLKDKVLKDSSVSRSTKCKLFNEWTLSQLAS--LYS 214 (330)
T ss_pred HHHHHccCCHHHHHHHHHcCchHHHHHhcccCCCH-HHHHHHHHHHHHHhccCCCCChhhhhhhcCHHHHHHHHH--Hhc
Confidence 1234555555532 4444444444432 3333 4444443111 344444566788888877666 555
Q ss_pred cCCccccccCcchHHHHHhhh
Q psy6184 134 IKGIDQIVDSSSSVALWLRHF 154 (156)
Q Consensus 134 ~~~~~q~~~~~~~~~~~~~~~ 154 (156)
.+|. +..++++-...+|
T Consensus 215 ~~~~----~~~~~~~~~vh~f 231 (330)
T PF11707_consen 215 RDGE----DEKSSVADLVHEF 231 (330)
T ss_pred ccCC----cccchHHHHHHHH
Confidence 5555 5666666555544
No 30
>KOG2057|consensus
Probab=80.52 E-value=7.8 Score=34.02 Aligned_cols=67 Identities=15% Similarity=0.245 Sum_probs=45.4
Q ss_pred HHHHHHHHhc---CCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhc-----c---CCcHHHHHHHHHHHH
Q psy6184 13 ALASIKKKLT---NSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVR-----G---TQHEEVKAKILELIQ 81 (156)
Q Consensus 13 AvraL~KrL~---~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~-----~---~~~~~Vk~kil~li~ 81 (156)
.+..|-.|+. ..+.+.++.+|.||+.|++|+.++|-++- ++-.=+|+.|-+ . .....||.|+.+++.
T Consensus 62 lmnmL~qRMLedNK~~WRRVYKSLiLLaYLikNGSER~VqeA--REh~YdLR~LEnYhfiDEhGKDQGINIR~kVKeilE 139 (499)
T KOG2057|consen 62 LMNMLFQRMLEDNKDAWRRVYKSLILLAYLIKNGSERFVQEA--REHAYDLRRLENYHFIDEHGKDQGINIRHKVKEILE 139 (499)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcccHHHHHHH--HHHHHHHHhhhhccchhhhCccccccHHHHHHHHHH
Confidence 3445556652 34678899999999999999999998875 444445555432 1 123557777777654
No 31
>KOG0251|consensus
Probab=79.06 E-value=2.8 Score=38.12 Aligned_cols=49 Identities=14% Similarity=0.238 Sum_probs=44.2
Q ss_pred CCChHHHHHHHHHHhcC-CCHHHHHHHHHHHHHHHHccchhHHhhhccHH
Q psy6184 7 TIVPSHALASIKKKLTN-SNPHIVLYALLVLESCVKNCGNLIHDEVGTKA 55 (156)
Q Consensus 7 ~~~~k~AvraL~KrL~~-~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~ 55 (156)
......++.+|-.||.+ +|.-|++-||-|+.-+++.+.+.|..++.+.-
T Consensus 55 ~~~i~~~v~aLs~Rl~~TrnW~VAlKsLIliH~ll~~G~~~f~~~l~~~~ 104 (491)
T KOG0251|consen 55 PASIPSCVHALSERLNKTRNWTVALKALILIHRLLKEGDPSFEQELLSRN 104 (491)
T ss_pred cccHHHHHHHHHHHhCCCcceeehHHHHHHHHHHHhcCcHHHHHHHHhcc
Confidence 35788999999999975 59999999999999999999999999988765
No 32
>KOG1293|consensus
Probab=76.66 E-value=15 Score=34.68 Aligned_cols=72 Identities=15% Similarity=0.188 Sum_probs=63.8
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHH
Q psy6184 14 LASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAHA 86 (156)
Q Consensus 14 vraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~ 86 (156)
+..|-+-+....+++--.++-+|--+|=||...+..+.-++=|.+-+..++++ ++..|++.++.+++...-.
T Consensus 463 Id~l~s~~~~~~~n~r~~~~~~Lr~l~f~~de~~k~~~~~ki~a~~i~~l~nd-~d~~Vqeq~fqllRNl~c~ 534 (678)
T KOG1293|consen 463 IDILESMLTDPDFNSRANSLWVLRHLMFNCDEEEKFQLLAKIPANLILDLIND-PDWAVQEQCFQLLRNLTCN 534 (678)
T ss_pred HHHHHHHhcCCCchHHHHHHHHHHHHHhcchHHHHHHHHHHhhHHHHHHHHhC-CCHHHHHHHHHHHHHhhcC
Confidence 55666777889999999999999999999999999999988888888888876 5788999999999998765
No 33
>smart00229 RasGEFN Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif. A subset of guanine nucleotide exchange factor for Ras-like small GTPases appear to possess this domain N-terminal to the RasGef (Cdc25-like) domain. The recent crystal structureof Sos shows that this domain is alpha-helical and plays a "purely structural role" (Nature 394, 337-343).
Probab=76.12 E-value=19 Score=25.70 Aligned_cols=73 Identities=16% Similarity=0.160 Sum_probs=47.3
Q ss_pred ChHHHHHHHHHHhcCCCH-----------HHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHH
Q psy6184 9 VPSHALASIKKKLTNSNP-----------HIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKIL 77 (156)
Q Consensus 9 ~~k~AvraL~KrL~~~n~-----------~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil 77 (156)
.|.+-+..|..|.....+ .++.+.+.++-.-+.|+...|..+-.-..++.++...+..........++.
T Consensus 41 tp~~ll~~L~~rf~~~~~~~~~~~~~~~~~~~~rv~~~l~~Wv~~~~~dF~~~~~l~~~l~~f~~~~~~~~~~~~~~~l~ 120 (127)
T smart00229 41 TTQELLQLLLYRYNAIPPESWVERKVNPLRVKNRVLNILRHWVENYWQDFEDDPKLILRLLEFLDLVDQEKGPGLVTSLQ 120 (127)
T ss_pred CHHHHHHHHHHHhCCCCcHHHHHHHhhHHHHHHHHHHHHHHHHHHCCcccccCHHHHHHHHHHHHHHhhCcCCCHHHHHH
Confidence 566777888888765433 267778888888889988888887655666666666554332333444454
Q ss_pred HHHH
Q psy6184 78 ELIQ 81 (156)
Q Consensus 78 ~li~ 81 (156)
++++
T Consensus 121 ~~~~ 124 (127)
T smart00229 121 ELLQ 124 (127)
T ss_pred HHHH
Confidence 4443
No 34
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=75.97 E-value=8.4 Score=26.67 Aligned_cols=70 Identities=11% Similarity=0.154 Sum_probs=44.6
Q ss_pred HHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHHhhCCCCCcchH-HHHHhhhCCCC
Q psy6184 36 LESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAHAFRNSPKYRAVP-TKSWMTDKGFK 108 (156)
Q Consensus 36 Le~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~F~~~~~l~~i~-~Y~~Lk~~Gi~ 108 (156)
|..+..|-|.....---.=.|-+.=+..++...+..+.+++.+|+..|.+......- +. +...|+.-|+.
T Consensus 5 L~~la~~LG~~W~~Lar~Lgls~~~I~~i~~~~p~~l~eQv~~mL~~W~~r~G~~AT---v~~L~~aL~~~~~~ 75 (83)
T cd08319 5 LNQLAQRLGPEWEQVLLDLGLSQTDIYRCKENHPHNVQSQIVEALVKWRQRFGKKAT---VQSLIQSLKAVEVD 75 (83)
T ss_pred HHHHHHHHhhhHHHHHHHcCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHHhcCCCCc---HHHHHHHHHHcCCC
Confidence 445566667665442222244444333343333456999999999999998765444 67 89999888864
No 35
>PF01602 Adaptin_N: Adaptin N terminal region; InterPro: IPR002553 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the N-terminal domain of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and from the beta and gamma subunits of various coatomer (COP) adaptors. This domain has a 2-layer alpha/alpha fold that forms a right-handed superhelix, and is a member of the ARM repeat superfamily []. The N-terminal region of the various AP adaptor proteins share strong sequence identity; by contrast, the C-terminal domains of different adaptins share similar structural folds, but have little sequence identity []. It has been proposed that the N-terminal domain interacts with another uniform component of the coated vesicles. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 1W63_C 2JKR_A 2JKT_A 2XA7_A 2VGL_B 3TJZ_E.
Probab=75.48 E-value=24 Score=30.92 Aligned_cols=88 Identities=18% Similarity=0.176 Sum_probs=56.2
Q ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHHhhC
Q psy6184 10 PSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAHAFRN 89 (156)
Q Consensus 10 ~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~F~~ 89 (156)
..-++.+|+|=|.++||.+...||..+-.+. .+. ++ ..+...+.+++.+ ++..||++++..+..-....++
T Consensus 77 ~~l~~n~l~kdl~~~n~~~~~lAL~~l~~i~---~~~----~~-~~l~~~v~~ll~~-~~~~VRk~A~~~l~~i~~~~p~ 147 (526)
T PF01602_consen 77 LILIINSLQKDLNSPNPYIRGLALRTLSNIR---TPE----MA-EPLIPDVIKLLSD-PSPYVRKKAALALLKIYRKDPD 147 (526)
T ss_dssp HHHHHHHHHHHHCSSSHHHHHHHHHHHHHH----SHH----HH-HHHHHHHHHHHHS-SSHHHHHHHHHHHHHHHHHCHC
T ss_pred HHHHHHHHHHhhcCCCHHHHHHHHhhhhhhc---ccc----hh-hHHHHHHHHHhcC-CchHHHHHHHHHHHHHhccCHH
Confidence 4558899999999999999999998776653 111 11 3345556666664 4568999888777766655443
Q ss_pred CCCCcchH-HHHHhhhCC
Q psy6184 90 SPKYRAVP-TKSWMTDKG 106 (156)
Q Consensus 90 ~~~l~~i~-~Y~~Lk~~G 106 (156)
...-..+. +.+.|....
T Consensus 148 ~~~~~~~~~l~~lL~d~~ 165 (526)
T PF01602_consen 148 LVEDELIPKLKQLLSDKD 165 (526)
T ss_dssp CHHGGHHHHHHHHTTHSS
T ss_pred HHHHHHHHHHhhhccCCc
Confidence 21101345 666665443
No 36
>PF11841 DUF3361: Domain of unknown function (DUF3361)
Probab=75.19 E-value=22 Score=27.74 Aligned_cols=59 Identities=22% Similarity=0.298 Sum_probs=47.0
Q ss_pred CCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHH
Q psy6184 24 SNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWA 84 (156)
Q Consensus 24 ~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa 84 (156)
.+++++..||.+||.+|.|... .+..|..+==++.|...+.. ++.+++...+.||-..-
T Consensus 72 ~d~~i~q~sLaILEs~Vl~S~~-ly~~V~~evt~~~Li~hLq~-~~~~iq~naiaLinAL~ 130 (160)
T PF11841_consen 72 MDASILQRSLAILESIVLNSPK-LYQLVEQEVTLESLIRHLQV-SNQEIQTNAIALINALF 130 (160)
T ss_pred ccchHHHHHHHHHHHHHhCCHH-HHHHHhccCCHHHHHHHHHc-CCHHHHHHHHHHHHHHH
Confidence 3799999999999999998654 35567766667778887776 67889999999987664
No 37
>KOG2071|consensus
Probab=74.97 E-value=4.1 Score=37.71 Aligned_cols=94 Identities=17% Similarity=0.300 Sum_probs=67.2
Q ss_pred CCChHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhc---cCCcHHHHHHHHHHHHHH
Q psy6184 7 TIVPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVR---GTQHEEVKAKILELIQAW 83 (156)
Q Consensus 7 ~~~~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~---~~~~~~Vk~kil~li~~W 83 (156)
.-.++..+.+|-++|...-|+.-|.++.++|..+||-|.+ .... |--.|..+.. ..+++..+.++..++..|
T Consensus 35 ~~~a~~iv~~iE~hi~kcpp~~kL~~~y~~dsi~knvg~p-y~~~----fs~~l~a~f~~~~~~vd~r~r~~l~~~~~tw 109 (579)
T KOG2071|consen 35 LPFAKSIVSAIEAHIAKCPPSQKLPVMYLLDSIVKNVGSP-YTTA----FSRNLVATFICAFTKVDERTRTSLFKLRATW 109 (579)
T ss_pred ccccHHHHHHHHHHHhhCCcccccchhhhhHHHHhhcCCc-chhh----hhhhHHHHHHHHHhhccccccchhHhhHHhh
Confidence 3456788999999999999999999999999999999999 3322 3333333332 246788899999999999
Q ss_pred HHHhhC---CCCCcchH---HHHHhhhC
Q psy6184 84 AHAFRN---SPKYRAVP---TKSWMTDK 105 (156)
Q Consensus 84 a~~F~~---~~~l~~i~---~Y~~Lk~~ 105 (156)
...-+. +|.+..+. .-+.|+..
T Consensus 110 ~~~~~~~sl~p~~~~~~~~~i~q~~~k~ 137 (579)
T KOG2071|consen 110 DLDPRSNSLDPAWSGVATSKIEQNLKKL 137 (579)
T ss_pred ccCCCCCCCCccCCccchhhhhhhhhhh
Confidence 944432 45555543 44444443
No 38
>PF07651 ANTH: ANTH domain; InterPro: IPR011417 AP180 is an endocytotic accessory protein that has been implicated in the formation of clathrin-coated pits. The domain is involved in phosphatidylinositol 4,5-bisphosphate binding and is a universal adaptor for nucleation of clathrin coats [, ].; GO: 0005543 phospholipid binding; PDB: 1HX8_A 3ZYM_A 1HFA_A 1HG2_A 3ZYL_B 3ZYK_A 1HG5_A 1HF8_A.
Probab=74.34 E-value=6.7 Score=32.06 Aligned_cols=47 Identities=15% Similarity=0.153 Sum_probs=39.2
Q ss_pred CCChHHHHHHHHHHhcCC-CHHHHHHHHHHHHHHHHccchhHHhhhcc
Q psy6184 7 TIVPSHALASIKKKLTNS-NPHIVLYALLVLESCVKNCGNLIHDEVGT 53 (156)
Q Consensus 7 ~~~~k~AvraL~KrL~~~-n~~v~l~AL~LLe~~vkNCG~~fh~eIas 53 (156)
+.+...++.+|.+|+... |+.|++-+|.++.-+++-+.+.|-.++..
T Consensus 34 ~~~~~~~~~~l~~Rl~~~~~w~V~~K~Lil~H~llr~G~~~~~~~~~~ 81 (280)
T PF07651_consen 34 PESVAFLFWALSRRLPLTRNWIVALKALILLHRLLRDGHPSFLQELLR 81 (280)
T ss_dssp TS-HHHHHHHHHHHCTSS-SHHHHHHHHHHHHHHHHHS-CHHHHHHHH
T ss_pred CccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHcCchHHHHHHHH
Confidence 467789999999999764 99999999999999999998887766654
No 39
>PF12348 CLASP_N: CLASP N terminal; InterPro: IPR024395 This domain is found in the N-terminal region of CLIP-associated proteins (CLASPs), which are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules [, ]. The domain is also found in other proteins involved in microtubule binding, including STU1, MOR1 and spindle pole body component Alp14.; PDB: 2QK2_A.
Probab=74.20 E-value=14 Score=28.89 Aligned_cols=70 Identities=10% Similarity=0.156 Sum_probs=47.9
Q ss_pred HHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHHhh
Q psy6184 16 SIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAHAFR 88 (156)
Q Consensus 16 aL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~F~ 88 (156)
.|.+.+.+.+..++..|+.++..+..++|..|... ...++..|.+.+.+. ..-|++.+...+..+.....
T Consensus 57 ~i~~~l~d~Rs~v~~~A~~~l~~l~~~l~~~~~~~--~~~~l~~Ll~~~~~~-~~~i~~~a~~~L~~i~~~~~ 126 (228)
T PF12348_consen 57 AIIKQLSDLRSKVSKTACQLLSDLARQLGSHFEPY--ADILLPPLLKKLGDS-KKFIREAANNALDAIIESCS 126 (228)
T ss_dssp HHHH-S-HH---HHHHHHHHHHHHHHHHGGGGHHH--HHHHHHHHHHGGG----HHHHHHHHHHHHHHHTTS-
T ss_pred HHHHHHhhhHHHHHHHHHHHHHHHHHHHhHhHHHH--HHHHHHHHHHHHccc-cHHHHHHHHHHHHHHHHHCC
Confidence 55577888889999999999999999999998776 367777777776653 35677777777777665443
No 40
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members
Probab=73.94 E-value=6.8 Score=27.05 Aligned_cols=68 Identities=13% Similarity=0.184 Sum_probs=39.8
Q ss_pred HHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHHhhCCCCCcchH-HHHHhhhCC
Q psy6184 37 ESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAHAFRNSPKYRAVP-TKSWMTDKG 106 (156)
Q Consensus 37 e~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~F~~~~~l~~i~-~Y~~Lk~~G 106 (156)
..+..|-|.....-.-.=.+-+.=+..++...+..+++++..|++.|.+.-++++. .+. +.+.|+.-|
T Consensus 6 ~~ia~~LG~~Wk~lar~LGlse~~Id~Ie~~~~~dl~eq~~~mL~~W~~~~~~~~a--tv~~L~~AL~~~g 74 (86)
T cd08779 6 LSIAGRLGLDWQAIGLHLGLSYRELQRIKYNNRDDLDEQIFDMLFSWAQRQAGDPD--AVGKLVTALEESG 74 (86)
T ss_pred HHHHHHHhHHHHHHHHHcCCCHHHHHHHHHHCccCHHHHHHHHHHHHHHhcCCCch--HHHHHHHHHHHcC
Confidence 34455666665332211133333333343322456999999999999998765433 255 777777655
No 41
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=72.09 E-value=9.2 Score=26.36 Aligned_cols=69 Identities=12% Similarity=0.206 Sum_probs=44.9
Q ss_pred HHHHHHHccchhHHhhhccHHHHHHHHH-hhccCCcHHHHHHHHHHHHHHHHHhhCCCCCcchH-HHHHhhhCCC
Q psy6184 35 VLESCVKNCGNLIHDEVGTKAFMEQMKE-LVRGTQHEEVKAKILELIQAWAHAFRNSPKYRAVP-TKSWMTDKGF 107 (156)
Q Consensus 35 LLe~~vkNCG~~fh~eIask~Fl~~l~k-l~~~~~~~~Vk~kil~li~~Wa~~F~~~~~l~~i~-~Y~~Lk~~Gi 107 (156)
..+.+.+|-|.....-.-.-.|-+.=+. +-.+++ ..+++++.+|+..|...-..... +. +.+.|+.-|.
T Consensus 4 ~f~~i~~~lG~~Wk~laR~LGlse~~Id~i~~~~~-~~~~eq~~~mL~~W~~~~g~~At---~~~L~~aL~~~~l 74 (86)
T cd08306 4 AFDVICENVGRDWRKLARKLGLSETKIESIEEAHP-RNLREQVRQSLREWKKIKKKEAK---VADLIKALRDCQL 74 (86)
T ss_pred HHHHHHHHHhhhHHHHHHHcCCCHHHHHHHHHHCC-CCHHHHHHHHHHHHHHhHCcchH---HHHHHHHHHHcCc
Confidence 4566777888776553333356555333 433444 46999999999999997654433 55 7777776654
No 42
>PF12783 Sec7_N: Guanine nucleotide exchange factor in Golgi transport N-terminal
Probab=70.85 E-value=43 Score=25.25 Aligned_cols=64 Identities=17% Similarity=0.290 Sum_probs=42.6
Q ss_pred CHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHH--------HhhccCCcHHHHHHHHHHHHHHHHHhhC
Q psy6184 25 NPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMK--------ELVRGTQHEEVKAKILELIQAWAHAFRN 89 (156)
Q Consensus 25 n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~--------kl~~~~~~~~Vk~kil~li~~Wa~~F~~ 89 (156)
+......+|.+++.+..|+|..|...=.-..|++-+. +.+.. .+..|-.+.+.++..--..|+.
T Consensus 35 ~~~~k~l~LeLl~~iL~~~~~~f~~~~~~~~l~~~lk~~l~~~Ll~~~~~-~~~~i~~~slri~~~l~~~~~~ 106 (168)
T PF12783_consen 35 DERSKLLSLELLESILENHGSVFRSSEEHPSLINLLKDDLCPALLKNLSS-SDFPIFSRSLRIFLTLLSRFRS 106 (168)
T ss_pred hHHHHHHHHHHHHHHHHhCHHHHhCCcchHHHHHHHHHHHHHHHHHHHhh-hhhHHHHHHHHHHHHHHHHHHH
Confidence 3467889999999999999998874111124444443 22222 3366777888887777777765
No 43
>PF02985 HEAT: HEAT repeat; InterPro: IPR000357 The HEAT repeat is a tandemly repeated, 37-47 amino acid long module occurring in a number of cytoplasmic proteins, including the four name-giving proteins huntingtin, elongation factor 3 (EF3), the 65 Kd alpha regulatory subunit of protein phosphatase 2A (PP2A) and the yeast PI3-kinase TOR1 []. Arrays of HEAT repeats consists of 3 to 36 units forming a rod-like helical structure and appear to function as protein-protein interaction surfaces. It has been noted that many HEAT repeat-containing proteins are involved in intracellular transport processes. In the crystal structure of PP2A PR65/A [], the HEAT repeats consist of pairs of antiparallel alpha helices [].; GO: 0005515 protein binding; PDB: 3FGA_A 2PF4_C 2IAE_A 2BKU_D 3EA5_B 3ND2_A 2BPT_A 2NYL_A 2NPP_D 2PKG_B ....
Probab=70.46 E-value=15 Score=19.99 Aligned_cols=30 Identities=20% Similarity=0.351 Sum_probs=25.1
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHHcc
Q psy6184 14 LASIKKKLTNSNPHIVLYALLVLESCVKNC 43 (156)
Q Consensus 14 vraL~KrL~~~n~~v~l~AL~LLe~~vkNC 43 (156)
+-.|.+-++++++.|-..|..-|..++++|
T Consensus 2 lp~l~~~l~D~~~~VR~~a~~~l~~i~~~~ 31 (31)
T PF02985_consen 2 LPILLQLLNDPSPEVRQAAAECLGAIAEHC 31 (31)
T ss_dssp HHHHHHHHT-SSHHHHHHHHHHHHHHHHTS
T ss_pred HHHHHHHcCCCCHHHHHHHHHHHHHHHhhC
Confidence 346778889999999999999999998887
No 44
>KOG1077|consensus
Probab=70.16 E-value=22 Score=34.21 Aligned_cols=61 Identities=31% Similarity=0.459 Sum_probs=45.6
Q ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhc-cCCcHHHHHHHHH
Q psy6184 10 PSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVR-GTQHEEVKAKILE 78 (156)
Q Consensus 10 ~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~-~~~~~~Vk~kil~ 78 (156)
-|.++..|++-|.++||.-+.+||. |+-|-|.+=-. ..|-+++-||+- ..+..-||++..-
T Consensus 109 ~klvin~iknDL~srn~~fv~LAL~----~I~niG~re~~----ea~~~DI~KlLvS~~~~~~vkqkaAL 170 (938)
T KOG1077|consen 109 MKLVINSIKNDLSSRNPTFVCLALH----CIANIGSREMA----EAFADDIPKLLVSGSSMDYVKQKAAL 170 (938)
T ss_pred HHHHHHHHHhhhhcCCcHHHHHHHH----HHHhhccHhHH----HHhhhhhHHHHhCCcchHHHHHHHHH
Confidence 4788999999999999999999996 77787766222 467777888774 4455667766543
No 45
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=69.52 E-value=41 Score=25.76 Aligned_cols=68 Identities=16% Similarity=0.235 Sum_probs=54.6
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHH
Q psy6184 13 ALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAHA 86 (156)
Q Consensus 13 AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~ 86 (156)
-+..|.++|.+++|.|-..|+.+|-.|+.|.=-++..++ +..+..++.+ ++++|++-+...+.+....
T Consensus 26 ~~~~l~~~L~D~~~~VR~~al~~Ls~Li~~d~ik~k~~l-----~~~~l~~l~D-~~~~Ir~~A~~~~~e~~~~ 93 (178)
T PF12717_consen 26 YLPNLYKCLRDEDPLVRKTALLVLSHLILEDMIKVKGQL-----FSRILKLLVD-ENPEIRSLARSFFSELLKK 93 (178)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCceeehhhh-----hHHHHHHHcC-CCHHHHHHHHHHHHHHHHh
Confidence 466888999999999999999999999998765555432 4566666644 5788999999999998876
No 46
>PF11698 V-ATPase_H_C: V-ATPase subunit H; InterPro: IPR011987 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. This entry represents the C-terminal domain of subunit H (also known as Vma13p) found in the V1 complex of V-ATPases. This subunit has a regulatory function, being responsible for activating ATPase activity and coupling ATPase activity to proton flow []. The yeast enzyme contains five motifs similar to the HEAT or Armadillo repeats seen in the importins, and can be divided into two distinct domains: a large N-terminal domain consisting of stacked alpha helices, and a smaller C-terminal alpha-helical domain with a similar superhelical topology to an armadillo repeat []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0015991 ATP hydrolysis coupled proton transport, 0000221 vacuolar proton-transporting V-type ATPase, V1 domain; PDB: 1HO8_A.
Probab=68.72 E-value=28 Score=25.84 Aligned_cols=72 Identities=19% Similarity=0.201 Sum_probs=46.6
Q ss_pred HHHHHHHHHHh-cCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHH
Q psy6184 11 SHALASIKKKL-TNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWA 84 (156)
Q Consensus 11 k~AvraL~KrL-~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa 84 (156)
=+.++.|.+-| .+.+|.++--|..=+...|+..... ...|..-..-+.+..++. +++.+||..+|..+|.+=
T Consensus 42 ~~llk~L~~lL~~s~d~~~laVac~Dig~~vr~~p~g-r~ii~~lg~K~~vM~Lm~-h~d~eVr~eAL~avQklm 114 (119)
T PF11698_consen 42 FELLKKLIKLLDKSDDPTTLAVACHDIGEFVRHYPNG-RNIIEKLGAKERVMELMN-HEDPEVRYEALLAVQKLM 114 (119)
T ss_dssp GHHHHHHHHHH-SHHHHHHHHHHHHHHHHHHHH-GGG-HHHHHHHSHHHHHHHHTS--SSHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHccCCCcceeehhhcchHHHHHHChhH-HHHHHhcChHHHHHHHhc-CCCHHHHHHHHHHHHHHH
Confidence 35788888888 5567888888888888888886443 111211122223445555 478999999999998763
No 47
>PF03385 DUF288: Protein of unknown function, DUF288; InterPro: IPR005049 This is a protein family of unknown function.
Probab=67.13 E-value=8.6 Score=33.90 Aligned_cols=86 Identities=17% Similarity=0.181 Sum_probs=63.7
Q ss_pred HHHHHHHHHHHHHHHH-HhhCCCCCcchH-HHHHhhhCCCCCCC--C-C-CCCCC--Chh----hhhhhhhccccccCCc
Q psy6184 70 EEVKAKILELIQAWAH-AFRNSPKYRAVP-TKSWMTDKGFKNPS--K-S-SDSLG--LEL----QIFRICHIHFSEIKGI 137 (156)
Q Consensus 70 ~~Vk~kil~li~~Wa~-~F~~~~~l~~i~-~Y~~Lk~~Gi~FP~--~-~-~~a~f--~~~----~~~~~~~~~~~~~~~~ 137 (156)
..+-++|++|-...++ .|=...+..++. .-+.|++=|+.||. . + .++.- +.+ --||..++.|-...-+
T Consensus 70 ~~L~~~Il~L~~~m~e~GfW~~~Dv~L~~AWL~DL~sVGY~fP~L~~~~~~dpYs~s~net~R~vNCRRm~leF~lvdp~ 149 (390)
T PF03385_consen 70 STLFECILDLYVAMAEEGFWGEEDVKLMQAWLQDLKSVGYKFPRLRSEEYRDPYSPSTNETSRDVNCRRMHLEFELVDPK 149 (390)
T ss_pred hhHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHHHHHhhchhhhhcccCCCCCCCCCccccccccccccceeeccCCc
Confidence 3577899998888887 566667777888 88999999999998 1 2 22221 111 2599999999999888
Q ss_pred cccccCcchHHHHHhhhc
Q psy6184 138 DQIVDSSSSVALWLRHFA 155 (156)
Q Consensus 138 ~q~~~~~~~~~~~~~~~~ 155 (156)
+....+-.-.+-+|.+|.
T Consensus 150 ~~~~~~~~ra~qKlnyFG 167 (390)
T PF03385_consen 150 KEESQNIKRAEQKLNYFG 167 (390)
T ss_pred ccccHHHHHHHHHHHhhc
Confidence 877776667777887774
No 48
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=66.55 E-value=20 Score=23.35 Aligned_cols=32 Identities=19% Similarity=0.357 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCcchH-HHHHhhhCC
Q psy6184 72 VKAKILELIQAWAHAFRNSPKYRAVP-TKSWMTDKG 106 (156)
Q Consensus 72 Vk~kil~li~~Wa~~F~~~~~l~~i~-~Y~~Lk~~G 106 (156)
+.+++.+++..|......+.. +. +...|+.-|
T Consensus 39 ~~~~~~~~L~~W~~~~~~~at---~~~L~~aL~~~~ 71 (83)
T PF00531_consen 39 LREQTYEMLQRWRQREGPNAT---VDQLIQALRDIG 71 (83)
T ss_dssp HHHHHHHHHHHHHHHHGSTSS---HHHHHHHHHHTT
T ss_pred hHHHHHHHHHHHHHhcCCCCc---HHHHHHHHHHCC
Confidence 999999999999999555555 55 777777655
No 49
>PTZ00429 beta-adaptin; Provisional
Probab=65.73 E-value=22 Score=34.07 Aligned_cols=44 Identities=16% Similarity=0.351 Sum_probs=34.8
Q ss_pred CCChHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhh
Q psy6184 7 TIVPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDE 50 (156)
Q Consensus 7 ~~~~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~e 50 (156)
+....+.+..+..+|+|.|+.|++-|..++=.+..+|....+.+
T Consensus 251 ~~e~~~il~~l~~~Lq~~N~AVVl~Aik~il~l~~~~~~~~~~~ 294 (746)
T PTZ00429 251 KESAETLLTRVLPRMSHQNPAVVMGAIKVVANLASRCSQELIER 294 (746)
T ss_pred cHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCcCCHHHHHH
Confidence 34456788899999999999999999998888877775544443
No 50
>PF09324 DUF1981: Domain of unknown function (DUF1981); InterPro: IPR015403 This domain is functionally uncharacterised and found in various plant and yeast protein transport proteins. It is noramlly associated with and C-termianl to the SEC7 domain. The SEC7 domain was named after the first protein found to contain such a region []. It has been shown to be linked with guanine nucleotide exchange function [, ].
Probab=65.65 E-value=13 Score=25.59 Aligned_cols=35 Identities=20% Similarity=0.286 Sum_probs=27.7
Q ss_pred HHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHHhh
Q psy6184 54 KAFMEQMKELVRGTQHEEVKAKILELIQAWAHAFR 88 (156)
Q Consensus 54 k~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~F~ 88 (156)
++|+.-+..++.+.++.+||+.+++.|..--....
T Consensus 16 ~~fL~Pf~~i~~~~~~~~vre~il~ci~qil~~~~ 50 (86)
T PF09324_consen 16 KDFLKPFEYIMSNNPSIDVRELILECILQILQSRG 50 (86)
T ss_pred HHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHHhH
Confidence 57777788888777889999999998877766544
No 51
>PRK01005 V-type ATP synthase subunit E; Provisional
Probab=63.90 E-value=41 Score=27.08 Aligned_cols=86 Identities=17% Similarity=0.120 Sum_probs=62.2
Q ss_pred HHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccC-CcHH-HHHHHHHHHHHHHHHhhC---------C--CC
Q psy6184 26 PHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGT-QHEE-VKAKILELIQAWAHAFRN---------S--PK 92 (156)
Q Consensus 26 ~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~-~~~~-Vk~kil~li~~Wa~~F~~---------~--~~ 92 (156)
....-++.+-++.-.++.-....+++.+.-|-..+.+++... .+++ +++.|++++..|.....+ . |+
T Consensus 63 e~ek~r~~s~a~l~~R~~~l~aKqevi~~vf~~a~~~lv~~~~~d~~~l~~lI~~~v~~~~~~~~~~~~~~~i~~~~~~~ 142 (207)
T PRK01005 63 DQKLKQGESALVQAGKRSLESLKQAVENKIFRESLGEWLEHVLTDPEVSAKLIQALVQAIEAQGISGNLTAYIGKHVSAR 142 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHhhcccccccchhhhhcCCHH
Confidence 344447888888888899888999999989999999999763 3555 688889999999875211 1 11
Q ss_pred -C-cchH--HHHHhhhCCCCCCC
Q psy6184 93 -Y-RAVP--TKSWMTDKGFKNPS 111 (156)
Q Consensus 93 -l-~~i~--~Y~~Lk~~Gi~FP~ 111 (156)
+ .++. +-+.|+++||.|-.
T Consensus 143 ~~~~~~~~~~~~~l~~~gv~~~~ 165 (207)
T PRK01005 143 AVNELLGKEVTKKLKEKGVSVGS 165 (207)
T ss_pred HHHHHHHHHHHHHHHHcCeEEec
Confidence 1 1233 56778899988754
No 52
>PF13513 HEAT_EZ: HEAT-like repeat; PDB: 2Z5J_A 2OT8_B 2Z5O_A 2H4M_A 2QMR_A 1QBK_B 2Z5M_A 2Z5K_A 2Z5N_A 1GCJ_B ....
Probab=62.47 E-value=26 Score=21.15 Aligned_cols=52 Identities=15% Similarity=0.262 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHH
Q psy6184 26 PHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELI 80 (156)
Q Consensus 26 ~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li 80 (156)
|.+...|+..|-.+..+|+..+... -.+.+..|..++++. +..||.....-+
T Consensus 1 p~vR~~A~~aLg~l~~~~~~~~~~~--~~~~~~~L~~~L~d~-~~~VR~~A~~aL 52 (55)
T PF13513_consen 1 PRVRRAAAWALGRLAEGCPELLQPY--LPELLPALIPLLQDD-DDSVRAAAAWAL 52 (55)
T ss_dssp HHHHHHHHHHHHCTTTTTHHHHHHH--HHHHHHHHHHHTTSS-SHHHHHHHHHHH
T ss_pred CHHHHHHHHHHhhHhcccHHHHHHH--HHHHHHHHHHHHcCC-CHHHHHHHHHHH
Confidence 4566677777777777887776552 256666677777654 448988775544
No 53
>PF12333 Ipi1_N: Rix1 complex component involved in 60S ribosome maturation; InterPro: IPR024679 This domain is found in IPI1, which is a component of the Rix1 complex involved in pre-rRNA-processing [, ]. It is also found in testis-expressed sequence 10 protein, a nuclear membrane protein, which is a component of the MLL1/MLL complex [].
Probab=60.14 E-value=58 Score=22.97 Aligned_cols=52 Identities=15% Similarity=0.221 Sum_probs=37.0
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhc
Q psy6184 13 ALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVR 65 (156)
Q Consensus 13 AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~ 65 (156)
.+-.|.-=+.|-+|.++.-|+.+||.++.+|+..+-.. ...+-++.+..++.
T Consensus 12 l~~~i~sAMTHi~~~Ir~dsl~~L~~lL~~~p~~~~~~-~~~kil~~f~~ll~ 63 (102)
T PF12333_consen 12 LMLYISSAMTHISPDIREDSLKFLDLLLEHAPDELCSG-GWVKILPNFLDLLG 63 (102)
T ss_pred HHHHHHHHHHhCCHHHHHhHHHHHHHHHHHCChHhHhh-hHHHHHHHHHHHHC
Confidence 34456666789999999999999999999999982221 12244555555653
No 54
>PF08328 ASL_C: Adenylosuccinate lyase C-terminal; InterPro: IPR013539 This domain is found at the C terminus of adenylosuccinate lyase(ASL; PurB in Escherichia coli). It has been identified in bacteria, eukaryotes and archaea and is found together with the lyase domain IPR000362 from INTERPRO. ASL catalyses the cleavage of succinylaminoimidazole carboxamide ribotide to aminoimidazole carboxamide ribotide and fumarate and the cleavage of adenylosuccinate to adenylate and fumarate []. ; GO: 0004018 N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity, 0006188 IMP biosynthetic process; PDB: 2HVG_A 2QGA_C 2PTS_A 2PTR_A 2PTQ_B 3BHG_A 3GZH_A.
Probab=59.35 E-value=44 Score=24.74 Aligned_cols=55 Identities=27% Similarity=0.342 Sum_probs=33.7
Q ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHH
Q psy6184 10 PSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILEL 79 (156)
Q Consensus 10 ~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~l 79 (156)
-.|++..+.+|-...||.+.+.+|+- |..+ +++=|.+++.-+ ..+.++|++++.|
T Consensus 55 laEpIQTvmRr~g~~~pYE~LK~lTR--------g~~i-----t~~~l~~fI~~L--~ip~~~k~~L~~l 109 (115)
T PF08328_consen 55 LAEPIQTVMRRYGIPNPYEKLKELTR--------GKKI-----TKEDLREFIESL--DIPEEAKARLLAL 109 (115)
T ss_dssp GHHHHHHHHHHTT-SSHHHHHHHHHT--------TS--------HHHHHHHHHTS--SS-HHHHHHHHH-
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHc--------CCCC-----CHHHHHHHHHhC--CCCHHHHHHHHhc
Confidence 35899999999999999999999972 3322 222222222222 3677888887765
No 55
>PF12783 Sec7_N: Guanine nucleotide exchange factor in Golgi transport N-terminal
Probab=59.31 E-value=74 Score=23.92 Aligned_cols=71 Identities=14% Similarity=0.195 Sum_probs=55.1
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHH-hhccC-CcHHHHHHHHHHHHHHHH
Q psy6184 13 ALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKE-LVRGT-QHEEVKAKILELIQAWAH 85 (156)
Q Consensus 13 AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~k-l~~~~-~~~~Vk~kil~li~~Wa~ 85 (156)
...+|.+-+.+.++.+..+++.++-.+..+-+..+..|+ .-|++.+.. ++... ++..-|.-+++.+..+..
T Consensus 74 l~~~Ll~~~~~~~~~i~~~slri~~~l~~~~~~~Lk~el--e~~l~~i~~~il~~~~~~~~~k~~~Le~l~~l~~ 146 (168)
T PF12783_consen 74 LCPALLKNLSSSDFPIFSRSLRIFLTLLSRFRSHLKLEL--EVFLSHIILRILESDNSSLWQKELALEILRELCK 146 (168)
T ss_pred HHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHccCCCcHHHHHHHHHHHHHHHh
Confidence 345666666677799999999999999999888888777 789999877 66543 345677888888887664
No 56
>PF01602 Adaptin_N: Adaptin N terminal region; InterPro: IPR002553 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the N-terminal domain of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and from the beta and gamma subunits of various coatomer (COP) adaptors. This domain has a 2-layer alpha/alpha fold that forms a right-handed superhelix, and is a member of the ARM repeat superfamily []. The N-terminal region of the various AP adaptor proteins share strong sequence identity; by contrast, the C-terminal domains of different adaptins share similar structural folds, but have little sequence identity []. It has been proposed that the N-terminal domain interacts with another uniform component of the coated vesicles. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 1W63_C 2JKR_A 2JKT_A 2XA7_A 2VGL_B 3TJZ_E.
Probab=59.29 E-value=58 Score=28.46 Aligned_cols=85 Identities=16% Similarity=0.275 Sum_probs=62.3
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHHhhCC
Q psy6184 11 SHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAHAFRNS 90 (156)
Q Consensus 11 k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~F~~~ 90 (156)
...+..+.+-+.+++|.|...|+.-+-.+.+.++..+.. . |.+.+.+++.+ .+..|+.-++.++... +..
T Consensus 113 ~~l~~~v~~ll~~~~~~VRk~A~~~l~~i~~~~p~~~~~----~-~~~~l~~lL~d-~~~~V~~~a~~~l~~i----~~~ 182 (526)
T PF01602_consen 113 EPLIPDVIKLLSDPSPYVRKKAALALLKIYRKDPDLVED----E-LIPKLKQLLSD-KDPSVVSAALSLLSEI----KCN 182 (526)
T ss_dssp HHHHHHHHHHHHSSSHHHHHHHHHHHHHHHHHCHCCHHG----G-HHHHHHHHTTH-SSHHHHHHHHHHHHHH----HCT
T ss_pred hHHHHHHHHHhcCCchHHHHHHHHHHHHHhccCHHHHHH----H-HHHHHhhhccC-CcchhHHHHHHHHHHH----ccC
Confidence 445667778889999999999998888888887665443 2 78899999965 4578988899998888 222
Q ss_pred CCC--cchH-HHHHhhhC
Q psy6184 91 PKY--RAVP-TKSWMTDK 105 (156)
Q Consensus 91 ~~l--~~i~-~Y~~Lk~~ 105 (156)
++. ..+. +|+.|.+-
T Consensus 183 ~~~~~~~~~~~~~~L~~~ 200 (526)
T PF01602_consen 183 DDSYKSLIPKLIRILCQL 200 (526)
T ss_dssp HHHHTTHHHHHHHHHHHH
T ss_pred cchhhhhHHHHHHHhhhc
Confidence 222 4556 77776643
No 57
>PF06798 PrkA: PrkA serine protein kinase C-terminal domain; InterPro: IPR010650 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This entry is found at the C terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length. PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.
Probab=59.23 E-value=15 Score=30.44 Aligned_cols=55 Identities=18% Similarity=0.263 Sum_probs=41.8
Q ss_pred CCCChHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccch--hHHhhhccHHHHHHHH
Q psy6184 6 WTIVPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGN--LIHDEVGTKAFMEQMK 61 (156)
Q Consensus 6 ~~~~~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~--~fh~eIask~Fl~~l~ 61 (156)
.+..|+++++.|..-+........+.++.||+.|...|.. .|..+. ..+|++-|.
T Consensus 35 ~GiS~R~~~~~ls~a~~~~~~~~~i~p~~vl~~L~~~l~~~~~i~~e~-~~~y~~~l~ 91 (254)
T PF06798_consen 35 SGISPRFVIKILSNALSSDSEEDCINPLDVLNELEEGLKDHPSISEEE-RERYLEFLK 91 (254)
T ss_pred CCCCHhHHHHHHHHHHHhCcccceecHHHHHHHHHHHhhcccccCHHH-HHHHHHHHH
Confidence 4678999999999999886677888899999999999988 344444 345555444
No 58
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (DDs) are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=58.45 E-value=26 Score=22.74 Aligned_cols=33 Identities=15% Similarity=0.279 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCcchH-HHHHhhhCCC
Q psy6184 72 VKAKILELIQAWAHAFRNSPKYRAVP-TKSWMTDKGF 107 (156)
Q Consensus 72 Vk~kil~li~~Wa~~F~~~~~l~~i~-~Y~~Lk~~Gi 107 (156)
+.+++.+|+..|.....++.. +. +++.|++-|.
T Consensus 37 ~~~~~~~mL~~W~~~~~~~at---~~~L~~aL~~~~~ 70 (79)
T cd01670 37 VREQAYQLLLKWEEREGDNAT---VGNLIEALREIGR 70 (79)
T ss_pred HHHHHHHHHHHHHhccCcCcH---HHHHHHHHHHcCH
Confidence 899999999999988765444 66 8888888775
No 59
>smart00005 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
Probab=57.93 E-value=16 Score=24.36 Aligned_cols=36 Identities=8% Similarity=0.230 Sum_probs=27.6
Q ss_pred cHHHHHHHHHHHHHHHHHhhCCCCCcchH-HHHHhhhCCC
Q psy6184 69 HEEVKAKILELIQAWAHAFRNSPKYRAVP-TKSWMTDKGF 107 (156)
Q Consensus 69 ~~~Vk~kil~li~~Wa~~F~~~~~l~~i~-~Y~~Lk~~Gi 107 (156)
+..+++.+..|+..|......+. .+. +...|+.-|.
T Consensus 42 ~~~~~~~~~~lL~~W~~~~g~~a---t~~~L~~aL~~~~~ 78 (88)
T smart00005 42 PRDLAEQSVQLLRLWEQREGKNA---TLGTLLEALRKMGR 78 (88)
T ss_pred CCCHHHHHHHHHHHHHHccchhh---HHHHHHHHHHHcCh
Confidence 34589999999999998865443 366 8888887764
No 60
>PF14816 FAM178: Family of unknown function, FAM178
Probab=57.92 E-value=1.1e+02 Score=27.03 Aligned_cols=111 Identities=15% Similarity=0.081 Sum_probs=65.6
Q ss_pred HHHHHHccchhHHhhhccHHHHHHHH--------------HhhccCCcHHHHHHHHHHHHHHHH--Hhh-CCC----CCc
Q psy6184 36 LESCVKNCGNLIHDEVGTKAFMEQMK--------------ELVRGTQHEEVKAKILELIQAWAH--AFR-NSP----KYR 94 (156)
Q Consensus 36 Le~~vkNCG~~fh~eIask~Fl~~l~--------------kl~~~~~~~~Vk~kil~li~~Wa~--~F~-~~~----~l~ 94 (156)
++.+.-.+|...+.......|+..+. +++.-.++..|..+++..+-.-+. .|. ++. =.+
T Consensus 118 le~l~l~S~~~qql~ll~~G~Ls~~Y~~~~CP~pll~WLFqlmsvh~d~~vs~~a~~~L~~is~~~~~~~s~~~~~~W~P 197 (377)
T PF14816_consen 118 LEKLFLSSSPAQQLFLLRSGLLSQLYLHQPCPVPLLQWLFQLMSVHPDCIVSSQALQTLWDISVDNLFRQSDEDSIPWCP 197 (377)
T ss_pred HHHHHhcCCHHHHHHHHHHHHHHHhhcCCCCChHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhccccccCCCCcCCccC
Confidence 34444456665555555555655544 344445667799999988766542 222 111 145
Q ss_pred chH-HHHHhhhCCCCCCC----CCCCCCCChhhhhhhhhccccccCCccccccCcch
Q psy6184 95 AVP-TKSWMTDKGFKNPS----KSSDSLGLELQIFRICHIHFSEIKGIDQIVDSSSS 146 (156)
Q Consensus 95 ~i~-~Y~~Lk~~Gi~FP~----~~~~a~f~~~~~~~~~~~~~~~~~~~~q~~~~~~~ 146 (156)
.+. ++.-+-+-|+.||. ...-+.|.++.+-.-++++..+-....|....+.|
T Consensus 198 Sl~di~~vf~nmGa~f~~L~pl~~~qp~f~e~~l~~~~~~s~~~q~~~~~~~~~~~s 254 (377)
T PF14816_consen 198 SLQDIAQVFVNMGASFPSLFPLGNLQPSFNERDLHSEIQLSVSEQQSIPQSCALDFS 254 (377)
T ss_pred CHHHHHHHHHHhcCCccccCcCCcCCCCcchhhhhhhccchhhccCCCccccccccC
Confidence 567 78888888998876 45566777776666555554444444455555555
No 61
>PRK09687 putative lyase; Provisional
Probab=57.31 E-value=85 Score=26.10 Aligned_cols=72 Identities=18% Similarity=0.269 Sum_probs=41.7
Q ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHHH---------HHHHcc--ch-hH-----HhhhccHHHHHHHHHhhccCCcHHH
Q psy6184 10 PSHALASIKKKLTNSNPHIVLYALLVLE---------SCVKNC--GN-LI-----HDEVGTKAFMEQMKELVRGTQHEEV 72 (156)
Q Consensus 10 ~k~AvraL~KrL~~~n~~v~l~AL~LLe---------~~vkNC--G~-~f-----h~eIask~Fl~~l~kl~~~~~~~~V 72 (156)
..+++..|.+.|...|+.|...|+.-|. .+++-- |. .+ --++++++.+..|..++...++..|
T Consensus 190 ~~~~~~~L~~~L~D~~~~VR~~A~~aLg~~~~~~av~~Li~~L~~~~~~~~a~~ALg~ig~~~a~p~L~~l~~~~~d~~v 269 (280)
T PRK09687 190 NPDIREAFVAMLQDKNEEIRIEAIIGLALRKDKRVLSVLIKELKKGTVGDLIIEAAGELGDKTLLPVLDTLLYKFDDNEI 269 (280)
T ss_pred CHHHHHHHHHHhcCCChHHHHHHHHHHHccCChhHHHHHHHHHcCCchHHHHHHHHHhcCCHhHHHHHHHHHhhCCChhH
Confidence 4466777777777777777666654332 222111 11 11 1345566777777777765567777
Q ss_pred HHHHHHHHH
Q psy6184 73 KAKILELIQ 81 (156)
Q Consensus 73 k~kil~li~ 81 (156)
+.++.+-++
T Consensus 270 ~~~a~~a~~ 278 (280)
T PRK09687 270 ITKAIDKLK 278 (280)
T ss_pred HHHHHHHHh
Confidence 777766554
No 62
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-associati
Probab=55.05 E-value=28 Score=23.54 Aligned_cols=66 Identities=6% Similarity=0.048 Sum_probs=37.8
Q ss_pred HHHHHccchhHHhhhccHHHHHH-HHHhhccCCcHHHHHHHHHHHHHHHHHhhCCCCCcchH-HHHHhhhCC
Q psy6184 37 ESCVKNCGNLIHDEVGTKAFMEQ-MKELVRGTQHEEVKAKILELIQAWAHAFRNSPKYRAVP-TKSWMTDKG 106 (156)
Q Consensus 37 e~~vkNCG~~fh~eIask~Fl~~-l~kl~~~~~~~~Vk~kil~li~~Wa~~F~~~~~l~~i~-~Y~~Lk~~G 106 (156)
..+.+|-|.....-...=.|-+. +..+-..+ +..+.+++..|+..|......... +. +...|++-|
T Consensus 8 ~~ia~~lG~dW~~LAr~Lg~~~~dI~~i~~~~-~~~~~eq~~~mL~~W~~r~g~~at---~~~L~~AL~~i~ 75 (84)
T cd08317 8 ADISNLLGSDWPQLARELGVSETDIDLIKAEN-PNSLAQQAQAMLKLWLEREGKKAT---GNSLEKALKKIG 75 (84)
T ss_pred HHHHHHHhhHHHHHHHHcCCCHHHHHHHHHHC-CCCHHHHHHHHHHHHHHhcCCcch---HHHHHHHHHHcC
Confidence 34445556554443332244433 33333333 344779999999999988554333 45 777776654
No 63
>cd06224 REM Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately N-terminal to the RasGef (Cdc25-like) domain. REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins with the REM domain include Sos1 and Sos2, which relay signals from tyrosine-kinase mediated signalling to Ras, RasGRP1-4, RasGRF1,2, CNrasGEF, and RAP-specific nucleotide exchange factors, to name a few.
Probab=53.72 E-value=41 Score=23.45 Aligned_cols=44 Identities=9% Similarity=0.327 Sum_probs=31.1
Q ss_pred HHhhhccHHHHHHHHHhhccCC-------------cHHHHHHHHHHHHHHHHHhhCC
Q psy6184 47 IHDEVGTKAFMEQMKELVRGTQ-------------HEEVKAKILELIQAWAHAFRNS 90 (156)
Q Consensus 47 fh~eIask~Fl~~l~kl~~~~~-------------~~~Vk~kil~li~~Wa~~F~~~ 90 (156)
++.-+.+.++++.|........ ...++.+|+.+++.|-+.+..+
T Consensus 28 yrsF~s~~~ll~~L~~rf~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~Wv~~~~~d 84 (122)
T cd06224 28 YRSFTTPTELLEKLIERYEIAPPENLEYNDWDKKKSKPIRLRVLNVLRTWVENYPYD 84 (122)
T ss_pred hhhhCCHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHhCCCc
Confidence 3444555677777776654321 2558999999999999998865
No 64
>smart00549 TAFH TAF homology. Domain in Drosophila nervy, CBFA2T1, human TAF105, human TAF130, and Drosophila TAF110. Also known as nervy homology region 1 (NHR1).
Probab=53.39 E-value=28 Score=24.78 Aligned_cols=33 Identities=18% Similarity=0.361 Sum_probs=26.7
Q ss_pred HHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHH
Q psy6184 54 KAFMEQMKELVRGTQHEEVKAKILELIQAWAHA 86 (156)
Q Consensus 54 k~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~ 86 (156)
+.|+..|+++-++....+|-+++.+||+..-++
T Consensus 6 k~FL~tLi~ls~~~~qpe~~~~Vr~LV~~L~~~ 38 (92)
T smart00549 6 KRFLTTLIQLSNDISQPEVAERVRTLVLGLVNG 38 (92)
T ss_pred HHHHHHHHHHhcCCCcchHHHHHHHHHHHHHhC
Confidence 689999999998754478888888888887654
No 65
>smart00229 RasGEFN Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif. A subset of guanine nucleotide exchange factor for Ras-like small GTPases appear to possess this domain N-terminal to the RasGef (Cdc25-like) domain. The recent crystal structureof Sos shows that this domain is alpha-helical and plays a "purely structural role" (Nature 394, 337-343).
Probab=53.29 E-value=39 Score=24.02 Aligned_cols=43 Identities=12% Similarity=0.325 Sum_probs=28.6
Q ss_pred HhhhccHHHHHHHHHhhccCCc----------HHHHHHHHHHHHHHHHHhhCC
Q psy6184 48 HDEVGTKAFMEQMKELVRGTQH----------EEVKAKILELIQAWAHAFRNS 90 (156)
Q Consensus 48 h~eIask~Fl~~l~kl~~~~~~----------~~Vk~kil~li~~Wa~~F~~~ 90 (156)
+.-+...++++.|.......++ ..++.+|+.+++.|-+.+..|
T Consensus 37 r~F~tp~~ll~~L~~rf~~~~~~~~~~~~~~~~~~~~rv~~~l~~Wv~~~~~d 89 (127)
T smart00229 37 RSFITTQELLQLLLYRYNAIPPESWVERKVNPLRVKNRVLNILRHWVENYWQD 89 (127)
T ss_pred hhhCCHHHHHHHHHHHhCCCCcHHHHHHHhhHHHHHHHHHHHHHHHHHHCCcc
Confidence 3334455666666665543222 348999999999999988753
No 66
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=52.23 E-value=31 Score=23.81 Aligned_cols=68 Identities=15% Similarity=0.167 Sum_probs=43.1
Q ss_pred HHHHHHccchhHHhhhccHHHHHHHHHhhc-cCCcHHHHHHHHHHHHHHHHHhh-CCCCCcchH-HHHHhhhCC
Q psy6184 36 LESCVKNCGNLIHDEVGTKAFMEQMKELVR-GTQHEEVKAKILELIQAWAHAFR-NSPKYRAVP-TKSWMTDKG 106 (156)
Q Consensus 36 Le~~vkNCG~~fh~eIask~Fl~~l~kl~~-~~~~~~Vk~kil~li~~Wa~~F~-~~~~l~~i~-~Y~~Lk~~G 106 (156)
++.+..|-|.....-.-.=.|-+.=++.+. .+....+++++.+|+..|..... .+.. +. +...|++-|
T Consensus 5 l~~l~~~lG~~Wk~lar~LG~s~~eI~~ie~~~~r~~~~eq~~~mL~~W~~r~g~~~AT---v~~L~~aL~~~~ 75 (86)
T cd08777 5 LDLLRENLGKKWKRCARKLGFTESEIEEIDHDYERDGLKEKVHQMLHKWKMKEGSKGAT---VGKLAQALEGCI 75 (86)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHhcccCCHHHHHHHHHHHHHHccCCCCcH---HHHHHHHHHHcc
Confidence 566677888875554333355555444444 33344589999999999998765 2333 55 777776544
No 67
>PF07531 TAFH: NHR1 homology to TAF; InterPro: IPR003894 The TAF homology (TAFH) or Nervy homology region 1 (NHR1) domain is a domain of 95-100 amino acids present in eukaryotic proteins of the MTG/ETO family and whereof the core ~75-80 residues occur in TAF proteins. The transcription initiation TFIID complex is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). The TAFH/NHR1 domain is named after fruit fly TATA-box-associated factor 110 (TAF110), human TAF105 and TAF130, and the fruit fly protein Nervy, which is a homologue of human MTG8/ETO [, ]. The human eight twenty-one (ETO or MTG8) and related myeloid transforming gene products MTGR1 and MTG16 as well as the Nervy protein contain the NHR1-4 domains. The NHR1/TAFH domain occurs in the N-terminal part of these proteins, while a MYND-type zinc finger forms the NHR4 domain []. The TAFH/NHR1 domain can be involved in protein-protein interactions, e.g in MTG8/ETO with HSP90 and Gfi-1 []. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2P6V_A 2KNH_A 2PP4_A 2H7B_A.
Probab=52.22 E-value=18 Score=25.88 Aligned_cols=33 Identities=27% Similarity=0.436 Sum_probs=26.5
Q ss_pred HHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHH
Q psy6184 54 KAFMEQMKELVRGTQHEEVKAKILELIQAWAHA 86 (156)
Q Consensus 54 k~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~ 86 (156)
+.|+..|+++.++....+|.+++.+||+..-++
T Consensus 7 k~FL~tLi~las~~~spev~~~Vr~LV~~L~~~ 39 (96)
T PF07531_consen 7 KNFLNTLIQLASDKQSPEVGENVRELVQNLVDG 39 (96)
T ss_dssp HHHHHHHHHHHCCSC-CCHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHhcCCCChHHHHHHHHHHHHHHcC
Confidence 689999999998866677888888888877654
No 68
>PF12755 Vac14_Fab1_bd: Vacuolar 14 Fab1-binding region
Probab=52.13 E-value=80 Score=22.15 Aligned_cols=63 Identities=16% Similarity=0.192 Sum_probs=44.4
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHH
Q psy6184 11 SHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKI 76 (156)
Q Consensus 11 k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~ki 76 (156)
++-+.-+.+-+...+++|-++|.+-|-.++|.++..+-.. -.+..+.|.+++.+ ++..||.-.
T Consensus 26 ~~Il~pVL~~~~D~d~rVRy~AcEaL~ni~k~~~~~~l~~--f~~IF~~L~kl~~D-~d~~Vr~~a 88 (97)
T PF12755_consen 26 DEILPPVLKCFDDQDSRVRYYACEALYNISKVARGEILPY--FNEIFDALCKLSAD-PDENVRSAA 88 (97)
T ss_pred HHHHHHHHHHcCCCcHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHcC-CchhHHHHH
Confidence 4456666777788999999999999999999998776431 13344445555554 566777654
No 69
>KOG1105|consensus
Probab=52.08 E-value=1e+02 Score=26.37 Aligned_cols=27 Identities=22% Similarity=0.527 Sum_probs=23.4
Q ss_pred hhccCCcHHHHHHHHHHHHHHHHHhhC
Q psy6184 63 LVRGTQHEEVKAKILELIQAWAHAFRN 89 (156)
Q Consensus 63 l~~~~~~~~Vk~kil~li~~Wa~~F~~ 89 (156)
.++..++++|+.++..||..|...+..
T Consensus 54 ~~Kk~~n~ev~~~ak~Lik~Wkk~~~~ 80 (296)
T KOG1105|consen 54 VLKKHKNEEVRSLAKKLIKSWKKLVDK 80 (296)
T ss_pred HHHhCCCHHHHHHHHHHHHHHHHHhhc
Confidence 445678999999999999999998864
No 70
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=52.04 E-value=41 Score=23.01 Aligned_cols=68 Identities=10% Similarity=0.167 Sum_probs=43.3
Q ss_pred HHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHHhhCCCCCcchH-HHHHhhhCCC
Q psy6184 36 LESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAHAFRNSPKYRAVP-TKSWMTDKGF 107 (156)
Q Consensus 36 Le~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~F~~~~~l~~i~-~Y~~Lk~~Gi 107 (156)
++.+..|-|.....-.-.=.|-+.=+.-+... +..+++++..|+..|...-..+.- +. +...|+.-|.
T Consensus 10 l~~ia~~iG~~Wk~Lar~LGls~~dI~~i~~~-~~~~~eq~~~mL~~W~~r~g~~AT---~~~L~~aL~~~~~ 78 (86)
T cd08318 10 ITVFANKLGEDWKTLAPHLEMKDKEIRAIESD-SEDIKMQAKQLLVAWQDREGSQAT---PETLITALNAAGL 78 (86)
T ss_pred HHHHHHHHhhhHHHHHHHcCCCHHHHHHHHhc-CCCHHHHHHHHHHHHHHhcCcccc---HHHHHHHHHHcCc
Confidence 34455777777666433335554433334322 235799999999999998665443 55 7777777664
No 71
>KOG2374|consensus
Probab=51.94 E-value=1e+02 Score=28.70 Aligned_cols=98 Identities=16% Similarity=0.361 Sum_probs=59.7
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchh--HHhhhccHHHHHH--HHHhh-c------------c-----CC-
Q psy6184 12 HALASIKKKLTNSNPHIVLYALLVLESCVKNCGNL--IHDEVGTKAFMEQ--MKELV-R------------G-----TQ- 68 (156)
Q Consensus 12 ~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~--fh~eIask~Fl~~--l~kl~-~------------~-----~~- 68 (156)
.-+++|+|-..+.+..+-+..=+|++.+-.|.... .-.+|...-||.. +..++ + + .+
T Consensus 26 ~~~k~lkkiv~~sdee~~~~~~~L~~~~~~~h~~vR~l~lqii~elF~rs~~FR~lii~n~~efLeL~~gt~p~~PLP~p 105 (661)
T KOG2374|consen 26 RLLKALKKIVRYSDEEVRLSSQTLMELMRHNHSQVRYLTLQIIDELFMRSKLFRTLIIENLDEFLELSIGTRPNLPLPAP 105 (661)
T ss_pred HHHHHHHHHHhccHHHHHHHHHHHHHHHhhcCchHHHHHHHHHHHHHHhhHHHHHHHHhCHHHHHHHhhcCCCCCCCCCC
Confidence 34677777777777665555556666666554332 2223333334322 11111 1 0 01
Q ss_pred ---cHHHHHHHHHHHHHHHHHhhCCCCCcchH-HHHHhhhC-CCCCCC
Q psy6184 69 ---HEEVKAKILELIQAWAHAFRNSPKYRAVP-TKSWMTDK-GFKNPS 111 (156)
Q Consensus 69 ---~~~Vk~kil~li~~Wa~~F~~~~~l~~i~-~Y~~Lk~~-Gi~FP~ 111 (156)
...+|.+..+.|..|-+.|.. .|+-+. .|.-||.- -+.||.
T Consensus 106 ~~~a~~Lr~~ai~~~e~Wnekfg~--~yk~l~lg~~~Lk~tkkvdf~d 151 (661)
T KOG2374|consen 106 PAVATTLRSKAIEFLEKWNEKFGF--HYKELRLGFDYLKNTKKVDFPD 151 (661)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhH--HHHHHHHHHHHHhccccccCcc
Confidence 256899999999999999973 355577 99999865 489997
No 72
>KOG4535|consensus
Probab=51.82 E-value=16 Score=33.89 Aligned_cols=32 Identities=16% Similarity=0.235 Sum_probs=28.4
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHHHHcc
Q psy6184 12 HALASIKKKLTNSNPHIVLYALLVLESCVKNC 43 (156)
Q Consensus 12 ~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNC 43 (156)
+.+..|++-|+|++|+|...||+|++++|.--
T Consensus 150 ~~~~~ik~~i~~~d~~v~vs~l~~~~~~v~t~ 181 (728)
T KOG4535|consen 150 KVWNQIKPYIRHKDVNVRVSSLTLLGAIVSTH 181 (728)
T ss_pred HHHHHHHHHhhcCCCChhhHHHHHHHHHHhcC
Confidence 46778999999999999999999999998653
No 73
>PF00618 RasGEF_N: RasGEF N-terminal motif; InterPro: IPR000651 The crystal structure of the guanine nucleotide exchange factor (GEF) region of human Sos1 complexes with Ras has been solved []. The structure consists of two distinct alpha helical structural domains: the N-terminal domain which seems to have a purely structural role and the C-terminal domain which is sufficient for catalytic activity and contains all residues that interact with Ras. A main feature of the catalytic domain is the protrusion of a helical hairpin important for the nucleotide-exchange mechanism. The N-terminal domain is likely to be important for the stability and correct placement of the hairpin structure. This entry represents a domain found in several GEF for Ras-like small GTPases which lies N-terminal to the RasGef (Cdc25-like) domain. ; GO: 0005085 guanyl-nucleotide exchange factor activity, 0051056 regulation of small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3CF6_E 2BYV_E 1NVW_S 1BKD_S 1XDV_A 2II0_A 1NVU_S 1NVX_S 1NVV_S 1XD4_B ....
Probab=51.33 E-value=43 Score=22.96 Aligned_cols=44 Identities=7% Similarity=0.308 Sum_probs=30.8
Q ss_pred HHhhhccHHHHHHHHHhhcc----CCc----------HHHHHHHHHHHHHHHHHhhCC
Q psy6184 47 IHDEVGTKAFMEQMKELVRG----TQH----------EEVKAKILELIQAWAHAFRNS 90 (156)
Q Consensus 47 fh~eIask~Fl~~l~kl~~~----~~~----------~~Vk~kil~li~~Wa~~F~~~ 90 (156)
++.-+.+.++++.|...... ... ..++.+|+.+|..|-+.+..|
T Consensus 33 yr~F~tp~~Ll~~L~~ry~~~~~~~~~~~~~~~~~~~~~i~~rv~~~l~~Wi~~~~~d 90 (104)
T PF00618_consen 33 YRSFTTPEELLDKLIQRYNIPPPNGLSQDESWDQDSQEPIRLRVLNVLKYWIENYPDD 90 (104)
T ss_dssp HHHCS-HHHHHHHHHHHHT---SSS-HHHHT-HHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred hHhhCCHHHHHHHHHHHhcccCCccccccchhhhhhhHHHHHHHHHHHHHHHHHChHh
Confidence 45666677888888877631 111 238889999999999998763
No 74
>PF10508 Proteasom_PSMB: Proteasome non-ATPase 26S subunit; InterPro: IPR019538 The 26S proteasome is an enzymatic complex that degrades ubiquitinated proteins in eukaryotic cells. 26S proteasome non-ATPase regulatory subunit 5 is one of a number of chaperones that are involved in the assembly of the proteasome. The chaperones dissociate before 26S proteasome formation is complete [].; GO: 0044183 protein binding involved in protein folding
Probab=51.22 E-value=85 Score=28.31 Aligned_cols=74 Identities=12% Similarity=0.166 Sum_probs=57.2
Q ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHH
Q psy6184 10 PSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAH 85 (156)
Q Consensus 10 ~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~ 85 (156)
.......|.+-|.|++|.|..+++..+.-|+.+-+. ....+.+.+.+..+...+.. ++..|.+.+..++..-+.
T Consensus 75 ~~~~~~~L~~gL~h~~~~Vr~l~l~~l~~~~~~~~~-~~~~~~~~~l~~~i~~~L~~-~d~~Va~~A~~~L~~l~~ 148 (503)
T PF10508_consen 75 LPQYQPFLQRGLTHPSPKVRRLALKQLGRIARHSEG-AAQLLVDNELLPLIIQCLRD-PDLSVAKAAIKALKKLAS 148 (503)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCHH-HHHHhcCccHHHHHHHHHcC-CcHHHHHHHHHHHHHHhC
Confidence 445566788888999999999999998888876654 45557777888887777753 577888888888877764
No 75
>PF12830 Nipped-B_C: Sister chromatid cohesion C-terminus
Probab=50.88 E-value=1.2e+02 Score=23.60 Aligned_cols=80 Identities=14% Similarity=0.203 Sum_probs=54.3
Q ss_pred HHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhcc-HHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHHhhCC--CC-
Q psy6184 17 IKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGT-KAFMEQMKELVRGTQHEEVKAKILELIQAWAHAFRNS--PK- 92 (156)
Q Consensus 17 L~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIas-k~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~F~~~--~~- 92 (156)
|.+-..+.++.+.+.|+.+++.+++.+ +.. .+-+-.++.|..+ ++..|+.++..++..-.+-+.+- ..
T Consensus 13 Il~~~~~~~~~vr~~Al~~l~~il~qG-------LvnP~~cvp~lIAL~ts-~~~~ir~~A~~~l~~l~eK~~s~v~~~~ 84 (187)
T PF12830_consen 13 ILELCLSSDDSVRLAALQVLELILRQG-------LVNPKQCVPTLIALETS-PNPSIRSRAYQLLKELHEKHESLVESRY 84 (187)
T ss_pred HHHHHhCCCHHHHHHHHHHHHHHHhcC-------CCChHHHHhHhhhhhCC-CChHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence 333446899999999999999999876 222 3455666676665 67889999988888887765531 11
Q ss_pred CcchH-HHHHhhh
Q psy6184 93 YRAVP-TKSWMTD 104 (156)
Q Consensus 93 l~~i~-~Y~~Lk~ 104 (156)
..+|+ +|+--++
T Consensus 85 ~~gi~~af~~~~~ 97 (187)
T PF12830_consen 85 SEGIRLAFDYQRR 97 (187)
T ss_pred HHHHHHHHHHHHH
Confidence 23455 5555444
No 76
>KOG1077|consensus
Probab=50.86 E-value=41 Score=32.50 Aligned_cols=70 Identities=14% Similarity=0.198 Sum_probs=44.5
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHH
Q psy6184 11 SHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWA 84 (156)
Q Consensus 11 k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa 84 (156)
..|+..|-+-|.|+.+|.-++||.-+- +=|...|-.+.-++. .+.+...++...+..|++|++.|+....
T Consensus 328 ~~~~~~Lg~fls~rE~NiRYLaLEsm~---~L~ss~~s~davK~h-~d~Ii~sLkterDvSirrravDLLY~mc 397 (938)
T KOG1077|consen 328 SRAVNQLGQFLSHRETNIRYLALESMC---KLASSEFSIDAVKKH-QDTIINSLKTERDVSIRRRAVDLLYAMC 397 (938)
T ss_pred HHHHHHHHHHhhcccccchhhhHHHHH---HHHhccchHHHHHHH-HHHHHHHhccccchHHHHHHHHHHHHHh
Confidence 456777888888888888888874333 333333333333333 6677777776667778888877776543
No 77
>cd00183 TFIIS_I N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme
Probab=50.21 E-value=59 Score=21.66 Aligned_cols=23 Identities=22% Similarity=0.491 Sum_probs=18.9
Q ss_pred ccCCcHHHHHHHHHHHHHHHHHh
Q psy6184 65 RGTQHEEVKAKILELIQAWAHAF 87 (156)
Q Consensus 65 ~~~~~~~Vk~kil~li~~Wa~~F 87 (156)
..+.+.+|+..+..++..|...+
T Consensus 53 rkh~~~~i~~~A~~Lv~~Wk~~v 75 (76)
T cd00183 53 RKHSNEKIRKLAKALIKSWKKLV 75 (76)
T ss_pred HcCCcHHHHHHHHHHHHHHHHhc
Confidence 34566999999999999998653
No 78
>PF04826 Arm_2: Armadillo-like; InterPro: IPR006911 This entry consists of mammalian proteins of unknown function.
Probab=49.73 E-value=1.3e+02 Score=24.93 Aligned_cols=76 Identities=12% Similarity=0.176 Sum_probs=56.9
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHHhhCC
Q psy6184 13 ALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAHAFRNS 90 (156)
Q Consensus 13 AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~F~~~ 90 (156)
.+..+-.=|.++|.+++.++|.+|=-+..|--- -+++-+.+-+..+..|+....+.++--+++.+++.-...++++
T Consensus 135 ~i~~ll~LL~~G~~~~k~~vLk~L~nLS~np~~--~~~Ll~~q~~~~~~~Lf~~~~~~~~l~~~l~~~~ni~~~~~~~ 210 (254)
T PF04826_consen 135 YIPDLLSLLSSGSEKTKVQVLKVLVNLSENPDM--TRELLSAQVLSSFLSLFNSSESKENLLRVLTFFENINENIKKE 210 (254)
T ss_pred hHHHHHHHHHcCChHHHHHHHHHHHHhccCHHH--HHHHHhccchhHHHHHHccCCccHHHHHHHHHHHHHHHhhCcc
Confidence 344454445789999999999999888766433 3333444557778888888888899999999999988888764
No 79
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=49.30 E-value=42 Score=23.21 Aligned_cols=67 Identities=7% Similarity=0.088 Sum_probs=43.9
Q ss_pred HHHHHHccchhHHhhhccHHHHHH-HHHhhccCCcHHHHHHHHHHHHHHHHHhhCCCCCcchH-HHHHhhhCC
Q psy6184 36 LESCVKNCGNLIHDEVGTKAFMEQ-MKELVRGTQHEEVKAKILELIQAWAHAFRNSPKYRAVP-TKSWMTDKG 106 (156)
Q Consensus 36 Le~~vkNCG~~fh~eIask~Fl~~-l~kl~~~~~~~~Vk~kil~li~~Wa~~F~~~~~l~~i~-~Y~~Lk~~G 106 (156)
++.+.+|-|.........-.|-+. +..+-..++ ..+.+++..++..|......+.. +. ++..|++-|
T Consensus 7 l~~Ia~~LG~dW~~Lar~L~vs~~dI~~I~~e~p-~~l~~Q~~~~L~~W~~r~g~~At---~~~L~~AL~~i~ 75 (84)
T cd08805 7 MAVIREHLGLSWAELARELQFSVEDINRIRVENP-NSLLEQSTALLNLWVDREGENAK---MSPLYPALYSID 75 (84)
T ss_pred HHHHHHHhcchHHHHHHHcCCCHHHHHHHHHhCC-CCHHHHHHHHHHHHHHhcCccch---HHHHHHHHHHCC
Confidence 455667777776654444455543 444444444 45999999999999998765544 55 777777654
No 80
>PF08767 CRM1_C: CRM1 C terminal; InterPro: IPR014877 CRM1 (also known as Exportin1) mediates the nuclear export of proteins bearing a leucine-rich nuclear export signal (NES). CRM1 forms a complex with the NES containing protein and the small GTPase Ran. This region forms an alpha helical structure formed by six helical hairpin motifs that are structurally similar to the HEAT repeat, but share little sequence similarity to the HEAT repeat []. ; PDB: 3M1I_C 3GB8_A 1W9C_A 3NC1_A 3NBY_D 3NBZ_D 3NC0_A 3GJX_D.
Probab=48.67 E-value=66 Score=27.31 Aligned_cols=54 Identities=13% Similarity=0.215 Sum_probs=42.0
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccch---hHHhhhccHHHHHHHHHhh
Q psy6184 11 SHALASIKKKLTNSNPHIVLYALLVLESCVKNCGN---LIHDEVGTKAFMEQMKELV 64 (156)
Q Consensus 11 k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~---~fh~eIask~Fl~~l~kl~ 64 (156)
+..+.+|.--++|.++++.-.+|..|..+++|+.. .+..+..+.-|++-+..++
T Consensus 164 ~~~idsi~wg~kh~~~~I~~~~L~~l~~ll~~~~~~~~~~~~~F~~~y~~~il~~if 220 (319)
T PF08767_consen 164 KLVIDSIVWGFKHTNREISETGLNILLELLNNVSKTNPEFANQFYQQYYLDILQDIF 220 (319)
T ss_dssp HHHHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHHH-SHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHH
Confidence 55677788888999999999999999999999988 6666666555555555443
No 81
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=48.38 E-value=39 Score=23.16 Aligned_cols=66 Identities=12% Similarity=0.123 Sum_probs=40.0
Q ss_pred HHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHHhhCCCCCcchH-HHHHhhh
Q psy6184 36 LESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAHAFRNSPKYRAVP-TKSWMTD 104 (156)
Q Consensus 36 Le~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~F~~~~~l~~i~-~Y~~Lk~ 104 (156)
|+.+.+|-|.....-.-.-.|-+.=+..++...+..+.+.+..|+..|...-..+.. +. ++..|++
T Consensus 7 l~~ia~~LG~dWk~LAr~Lg~se~dI~~i~~~~~~~~~eq~~~mL~~W~~r~g~~At---~~~L~~aL~~ 73 (84)
T cd08804 7 LAVIADHLGFSWTELARELDFTEEQIHQIRIENPNSLQDQSHALLKYWLERDGKHAT---DTNLMKCLTK 73 (84)
T ss_pred HHHHHHHHhhhHHHHHHHcCCCHHHHHHHHHHCcccHHHHHHHHHHHHHHccCCCch---HHHHHHHHHH
Confidence 344557777775543333355555444444333456999999999999987654444 44 5555554
No 82
>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere).
Probab=47.91 E-value=82 Score=21.02 Aligned_cols=22 Identities=23% Similarity=0.516 Sum_probs=19.0
Q ss_pred cCCcHHHHHHHHHHHHHHHHHh
Q psy6184 66 GTQHEEVKAKILELIQAWAHAF 87 (156)
Q Consensus 66 ~~~~~~Vk~kil~li~~Wa~~F 87 (156)
.+++.+|+..+.++|..|...+
T Consensus 52 kh~~~~I~~~A~~Li~~WK~~v 73 (75)
T smart00509 52 KHKNEEIRKLAKKLIKSWKKLV 73 (75)
T ss_pred cCCcHHHHHHHHHHHHHHHHHh
Confidence 3568999999999999998765
No 83
>PF14663 RasGEF_N_2: Rapamycin-insensitive companion of mTOR RasGEF_N domain
Probab=47.10 E-value=69 Score=23.09 Aligned_cols=29 Identities=24% Similarity=0.407 Sum_probs=25.1
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHH
Q psy6184 11 SHALASIKKKLTNSNPHIVLYALLVLESC 39 (156)
Q Consensus 11 k~AvraL~KrL~~~n~~v~l~AL~LLe~~ 39 (156)
+=+++.|.+.|...++.|+..|+.+|+-+
T Consensus 7 ~w~i~lLv~QL~D~~~~V~~~A~~iL~e~ 35 (115)
T PF14663_consen 7 DWGIELLVTQLYDPSPEVVAAALEILEEA 35 (115)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHH
Confidence 34788999999999999999999988764
No 84
>PF07197 DUF1409: Protein of unknown function (DUF1409); InterPro: IPR010811 This represents a short conserved region (approximately 50 residues long), sometimes repeated, within a number of hypothetical Oryza sativa proteins of unknown function.
Probab=46.81 E-value=21 Score=22.68 Aligned_cols=30 Identities=20% Similarity=0.354 Sum_probs=17.0
Q ss_pred HHHHHHccchh-HHhhhccHHHHHHHHHhhc
Q psy6184 36 LESCVKNCGNL-IHDEVGTKAFMEQMKELVR 65 (156)
Q Consensus 36 Le~~vkNCG~~-fh~eIask~Fl~~l~kl~~ 65 (156)
||.+|-|||.- -+.+=+....-+++.+++.
T Consensus 7 ld~lv~~cg~IrarleE~qa~i~~e~~~l~~ 37 (51)
T PF07197_consen 7 LDLLVVDCGSIRARLEEIQAQIPDELAKLAT 37 (51)
T ss_pred HHHHHhccchHHHHHHHHHHHhhHHHHHhcC
Confidence 78999999984 1222223344445555543
No 85
>KOG0915|consensus
Probab=45.62 E-value=1.2e+02 Score=31.66 Aligned_cols=83 Identities=23% Similarity=0.266 Sum_probs=60.9
Q ss_pred CCCCChHHHHHHHHHHh-cCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHH
Q psy6184 5 EWTIVPSHALASIKKKL-TNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAW 83 (156)
Q Consensus 5 ~~~~~~k~AvraL~KrL-~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~W 83 (156)
|+..+-.+|+..|=+-| ..+.-.|-.+.-.+++-|+.||+.+--+- ...=.-.|..|+.+++..++++++. .-|
T Consensus 1009 DP~~~Vq~aM~sIW~~Li~D~k~~vd~y~neIl~eLL~~lt~kewRV--ReasclAL~dLl~g~~~~~~~e~lp---elw 1083 (1702)
T KOG0915|consen 1009 DPDKKVQDAMTSIWNALITDSKKVVDEYLNEILDELLVNLTSKEWRV--REASCLALADLLQGRPFDQVKEKLP---ELW 1083 (1702)
T ss_pred CCcHHHHHHHHHHHHHhccChHHHHHHHHHHHHHHHHHhccchhHHH--HHHHHHHHHHHHcCCChHHHHHHHH---HHH
Confidence 56677788888888877 44566677888899999999998874431 1223455778888888888999888 668
Q ss_pred HHHhhCCCC
Q psy6184 84 AHAFRNSPK 92 (156)
Q Consensus 84 a~~F~~~~~ 92 (156)
-.+|+--.|
T Consensus 1084 ~~~fRvmDD 1092 (1702)
T KOG0915|consen 1084 EAAFRVMDD 1092 (1702)
T ss_pred HHHHHHHHH
Confidence 888884333
No 86
>KOG0946|consensus
Probab=45.13 E-value=42 Score=32.74 Aligned_cols=77 Identities=14% Similarity=0.256 Sum_probs=57.7
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccH-HHHHHHHHhhccCCcHHHHHHHHHHHHHHHHHhh
Q psy6184 11 SHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTK-AFMEQMKELVRGTQHEEVKAKILELIQAWAHAFR 88 (156)
Q Consensus 11 k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask-~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~F~ 88 (156)
+|-|..+.--+.+.|=+|-++|+.|+.+++++-|...+..+-.. -=+..|+.++.+ ..+.||+-.+-|+.+...+-.
T Consensus 121 qd~I~lll~~~e~~DF~VR~~aIqLlsalls~r~~e~q~~ll~~P~gIS~lmdlL~D-srE~IRNe~iLlL~eL~k~n~ 198 (970)
T KOG0946|consen 121 QDNITLLLQSLEEFDFHVRLYAIQLLSALLSCRPTELQDALLVSPMGISKLMDLLRD-SREPIRNEAILLLSELVKDNS 198 (970)
T ss_pred chhHHHHHHHHHhhchhhhhHHHHHHHHHHhcCCHHHHHHHHHCchhHHHHHHHHhh-hhhhhchhHHHHHHHHHccCc
Confidence 45566777777888999999999999999999999998877532 334556666654 356688888888887765533
No 87
>PF04826 Arm_2: Armadillo-like; InterPro: IPR006911 This entry consists of mammalian proteins of unknown function.
Probab=44.04 E-value=1.3e+02 Score=24.86 Aligned_cols=70 Identities=21% Similarity=0.267 Sum_probs=48.2
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHh-hccCCcHHHHHHHHHHHHHHHHHh
Q psy6184 14 LASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKEL-VRGTQHEEVKAKILELIQAWAHAF 87 (156)
Q Consensus 14 vraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl-~~~~~~~~Vk~kil~li~~Wa~~F 87 (156)
+-.|.+-|.+++|.+...||..|+.+ +.....+..| +.+++.+.+. ++...+..++.-.+.++...+...
T Consensus 56 i~lI~~lL~~p~~~vr~~AL~aL~Nl--s~~~en~~~I--k~~i~~Vc~~~~s~~lns~~Q~agLrlL~nLtv~~ 126 (254)
T PF04826_consen 56 ISLIGSLLNDPNPSVREKALNALNNL--SVNDENQEQI--KMYIPQVCEETVSSPLNSEVQLAGLRLLTNLTVTN 126 (254)
T ss_pred HHHHHHHcCCCChHHHHHHHHHHHhc--CCChhhHHHH--HHHHHHHHHHHhcCCCCCHHHHHHHHHHHccCCCc
Confidence 34677888999999999999999877 4444455555 5677776654 444456677777777777665443
No 88
>PLN03200 cellulose synthase-interactive protein; Provisional
Probab=43.60 E-value=83 Score=33.82 Aligned_cols=71 Identities=15% Similarity=0.134 Sum_probs=57.9
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHH
Q psy6184 13 ALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWA 84 (156)
Q Consensus 13 AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa 84 (156)
++..|..-|.+.++.+|..|..+|-.++.++++. ...|.....+..|++++++.++..||+.....+..-+
T Consensus 190 aVp~LV~LLsS~d~~lQ~eAa~aLa~Lass~ee~-~~aVIeaGaVP~LV~LL~sg~~~~VRE~AA~AL~nLA 260 (2102)
T PLN03200 190 GVDILVKLLSSGNSDAQANAASLLARLMMAFESS-ISKVLDAGAVKQLLKLLGQGNEVSVRAEAAGALEALS 260 (2102)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHcCChHH-HHHHHHCCCHHHHHHHHccCCChHHHHHHHHHHHHHh
Confidence 5667777888999999999999999999998875 5556667788999999977667789999888876655
No 89
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=42.69 E-value=20 Score=18.94 Aligned_cols=18 Identities=22% Similarity=0.110 Sum_probs=13.1
Q ss_pred CCCcchH-HHHHhhhCCCC
Q psy6184 91 PKYRAVP-TKSWMTDKGFK 108 (156)
Q Consensus 91 ~~l~~i~-~Y~~Lk~~Gi~ 108 (156)
.+..... +|+.++++|+.
T Consensus 15 g~~~~a~~~~~~M~~~gv~ 33 (34)
T PF13812_consen 15 GDPDAALQLFDEMKEQGVK 33 (34)
T ss_pred CCHHHHHHHHHHHHHhCCC
Confidence 3444566 99999999975
No 90
>PF14852 Fis1_TPR_N: Fis1 N-terminal tetratricopeptide repeat; PDB: 1IYG_A 3UUX_C 1Y8M_A 2PQR_A 2PQN_A 3O48_A 1PC2_A 1NZN_A.
Probab=40.92 E-value=23 Score=20.53 Aligned_cols=23 Identities=13% Similarity=0.124 Sum_probs=19.6
Q ss_pred hcCCCHHHHHHHHHHHHHHHHcc
Q psy6184 21 LTNSNPHIVLYALLVLESCVKNC 43 (156)
Q Consensus 21 L~~~n~~v~l~AL~LLe~~vkNC 43 (156)
+++++++.|...+.||+.+.++.
T Consensus 12 v~S~~~~d~~~Gi~lLe~l~~~~ 34 (35)
T PF14852_consen 12 VKSNNREDQQEGIALLEELYRDE 34 (35)
T ss_dssp HHSSSHHHHHHHHHHHHHHCCCS
T ss_pred hcCCCHHHHHHHHHHHHHHHhcc
Confidence 46899999999999999987653
No 91
>smart00543 MIF4G Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)
Probab=39.97 E-value=66 Score=24.03 Aligned_cols=36 Identities=17% Similarity=0.325 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhh
Q psy6184 28 IVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELV 64 (156)
Q Consensus 28 v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~ 64 (156)
.....+.++=.+...||..+... ..++.++++...+
T Consensus 135 ~~~~~ve~l~~lL~~~G~~l~~~-~~~~~~~~~l~~l 170 (200)
T smart00543 135 RSDFSVECLLSLLPTCGKDLERE-KSPKLLDEILERL 170 (200)
T ss_pred CcHHHHHHHHHHHHHhhHHHcCc-ccHHHHHHHHHHH
Confidence 34567777778888999998842 3466666665544
No 92
>PF11841 DUF3361: Domain of unknown function (DUF3361)
Probab=39.50 E-value=1.1e+02 Score=23.73 Aligned_cols=38 Identities=21% Similarity=0.285 Sum_probs=30.7
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhh
Q psy6184 14 LASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEV 51 (156)
Q Consensus 14 vraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eI 51 (156)
+..|-+-|+..|+..|..|+.|+.++..++++.=.+++
T Consensus 104 ~~~Li~hLq~~~~~iq~naiaLinAL~~kA~~~~r~~i 141 (160)
T PF11841_consen 104 LESLIRHLQVSNQEIQTNAIALINALFLKADDSKRKEI 141 (160)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHhcCChHHHHHH
Confidence 44566777789999999999999999999988644433
No 93
>KOG2025|consensus
Probab=37.20 E-value=1.1e+02 Score=29.81 Aligned_cols=62 Identities=18% Similarity=0.290 Sum_probs=45.2
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHH
Q psy6184 14 LASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQ 81 (156)
Q Consensus 14 vraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~ 81 (156)
...|.+||..+-|+|-+.|+..|--+=---+.. ..+-.|.+..++.+.++.+||+-+|..|.
T Consensus 128 ~e~l~~Rl~Drep~VRiqAv~aLsrlQ~d~~de------e~~v~n~l~~liqnDpS~EVRRaaLsnI~ 189 (892)
T KOG2025|consen 128 NEKLLIRLKDREPNVRIQAVLALSRLQGDPKDE------ECPVVNLLKDLIQNDPSDEVRRAALSNIS 189 (892)
T ss_pred HHHHHHHHhccCchHHHHHHHHHHHHhcCCCCC------cccHHHHHHHHHhcCCcHHHHHHHHHhhc
Confidence 457788999999999999998776553111110 12456778888888888999999888774
No 94
>PF08579 RPM2: Mitochondrial ribonuclease P subunit (RPM2); InterPro: IPR013888 Ribonuclease P (RNase P) generates mature tRNA molecules by cleaving their 5' ends. Rpm2 is a protein subunit of the yeast mitochondrial RNase P. It has the ability to act as a transcriptional activator in the nucleus, where it plays a role in defining the steady-state levels of mRNAs for some nucleus-encoded mitochondrial components. Rpm2p is also involved in maturation of Rpm1 and in translation of mitochondrial mRNAs [, , ].
Probab=36.27 E-value=63 Score=24.11 Aligned_cols=21 Identities=19% Similarity=0.333 Sum_probs=18.8
Q ss_pred CCCcchH-HHHHhhhCCCCCCC
Q psy6184 91 PKYRAVP-TKSWMTDKGFKNPS 111 (156)
Q Consensus 91 ~~l~~i~-~Y~~Lk~~Gi~FP~ 111 (156)
.+|..|. +|+.|||.|+.-|+
T Consensus 39 ~d~N~I~~lYqslkRN~i~lPs 60 (120)
T PF08579_consen 39 EDYNIINPLYQSLKRNGITLPS 60 (120)
T ss_pred cchHHHHHHHHHHHhcCCCCCc
Confidence 5788899 99999999998887
No 95
>PF11701 UNC45-central: Myosin-binding striated muscle assembly central; InterPro: IPR024660 The UNC-45 or small muscle protein 1 of Caenorhabditis elegans is expressed in two forms from different genomic positions in mammals: as a general tissue protein (UNC-45a) and as a specific form (UNC-45b) expressed only in striated and skeletal muscle. Myofibril formation requires both UNC-45 forms, consistent with the fact that the cytoskeleton is necessary for the development and maintenance of organised myofibrils []. Rng3 (Ring assembly protein 3), the homologue in Schizosaccharomyces pombe, is crucial for cell shape, normal actin cytoskeleton, and contractile ring assembly, and is essential for assembly of the myosin II-containing progenitors of the contractile ring. Widespread defects in the cytoskeleton are found in null mutants of all three fungal proteins []. Mammalian Unc45 is found to act as a specific chaperone during the folding of myosin and the assembly of striated muscle by forming a stable complex with the general chaperone Hsp90 []. All members carry up to three amino-terminal tetratricopeptide repeat (TPR) and a UCS domain at the C terminus that contains a number of Arm repeats. ; PDB: 3OPB_A 3NOW_A.
Probab=35.39 E-value=32 Score=26.11 Aligned_cols=68 Identities=16% Similarity=0.213 Sum_probs=40.0
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhc-cCCcHHHHHHHHHHHH
Q psy6184 14 LASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVR-GTQHEEVKAKILELIQ 81 (156)
Q Consensus 14 vraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~-~~~~~~Vk~kil~li~ 81 (156)
-..|.-++........+.++.++.+|.-=....-...+.+..|++.|..++. ...+..+..-++++|-
T Consensus 45 ~~~i~~~~~~~~~d~~i~~~~~l~~lfp~~~dv~~~l~~~eg~~~~l~~~~~~~~~~~~~~~~~lell~ 113 (157)
T PF11701_consen 45 SDFIESLLDEGEMDSLIIAFSALTALFPGPPDVGSELFLSEGFLESLLPLASRKSKDRKVQKAALELLS 113 (157)
T ss_dssp HHHHHHHHCCHHCCHHHHHHHHHHHHCTTTHHHHHHHCCTTTHHHHHHHHHH-CTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHccccchhHHHHHHHHHHHhCCCHHHHHHHHhhhhHHHHHHHHHhcccCCHHHHHHHHHHHH
Confidence 3444555544444456666666666655554455555566777777777776 3445666666666654
No 96
>PF14500 MMS19_N: Dos2-interacting transcription regulator of RNA-Pol-II
Probab=35.23 E-value=2.6e+02 Score=23.12 Aligned_cols=77 Identities=13% Similarity=0.201 Sum_probs=51.6
Q ss_pred hHHHHHHHHHHh--cCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHHh
Q psy6184 10 PSHALASIKKKL--TNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAHAF 87 (156)
Q Consensus 10 ~k~AvraL~KrL--~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~F 87 (156)
+...++.|-+.. +..-..+=+..+.+++.++.|-....+ .+ ..+|+..+..++.+-.|++.=-.+.+++..-...|
T Consensus 78 ~~~i~~~l~~~~~~q~~~q~~R~~~~~ll~~l~~~~~~~l~-~~-~~~fv~~~i~~~~gEkDPRnLl~~F~l~~~i~~~~ 155 (262)
T PF14500_consen 78 AVKILRSLFQNVDVQSLPQSTRYAVYQLLDSLLENHREALQ-SM-GDDFVYGFIQLIDGEKDPRNLLLSFKLLKVILQEF 155 (262)
T ss_pred HHHHHHHHHHhCChhhhhHHHHHHHHHHHHHHHHHhHHHHH-hc-hhHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHhc
Confidence 444455554443 234456667788999999999766652 23 46899999999987666665555666666666666
Q ss_pred h
Q psy6184 88 R 88 (156)
Q Consensus 88 ~ 88 (156)
.
T Consensus 156 ~ 156 (262)
T PF14500_consen 156 D 156 (262)
T ss_pred c
Confidence 5
No 97
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=34.38 E-value=1.7e+02 Score=20.75 Aligned_cols=97 Identities=15% Similarity=0.207 Sum_probs=58.9
Q ss_pred hHHHHHHHHHHh-cCCCHHHHHHHHHHHHHHHH--ccch-hHHhhhccHHHHHHHHH-hhccCCcHHHHHHHHHHHHHHH
Q psy6184 10 PSHALASIKKKL-TNSNPHIVLYALLVLESCVK--NCGN-LIHDEVGTKAFMEQMKE-LVRGTQHEEVKAKILELIQAWA 84 (156)
Q Consensus 10 ~k~AvraL~KrL-~~~n~~v~l~AL~LLe~~vk--NCG~-~fh~eIask~Fl~~l~k-l~~~~~~~~Vk~kil~li~~Wa 84 (156)
+.+++..+..+| ..+--+-..+|-..+...+. .-|+ .+..++..+..-.+++. .+.. .+ =.+.+..+++.+.
T Consensus 7 ~~e~I~~vi~~l~~~gyidD~~ya~~~v~~~~~~~~~G~~~I~~~L~~kGi~~~~i~~~l~~-~~--~~e~a~~~~~kk~ 83 (121)
T PF02631_consen 7 SEEAIEEVIDRLKELGYIDDERYAESYVRSRLRRKGKGPRRIRQKLKQKGIDREIIEEALEE-YD--EEEEALELAEKKY 83 (121)
T ss_dssp -HHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHTT--HHHHHHHHHHTT--HHHHHHHHTC-S---HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcccccccHHHHHHHHHHHCCChHHHHHHHHH-hh--HHHHHHHHHHHHH
Confidence 556666666676 46678889999999999884 3333 46677766666655443 3442 22 1222777777777
Q ss_pred HHhhCCCCCcchH-HHHHhhhCCCCC
Q psy6184 85 HAFRNSPKYRAVP-TKSWMTDKGFKN 109 (156)
Q Consensus 85 ~~F~~~~~l~~i~-~Y~~Lk~~Gi~F 109 (156)
......+...... ++..|.++|+.+
T Consensus 84 ~~~~~~~~~~~~~K~~~~L~rrGF~~ 109 (121)
T PF02631_consen 84 RRYRKPSDRKRKQKLIRFLMRRGFSY 109 (121)
T ss_dssp HHTTTS-CHHHHHHHHHHHHHTT--H
T ss_pred hcccCCCCHHHHHHHHHHHHHCCCCH
Confidence 7664445555667 999999999864
No 98
>KOG0132|consensus
Probab=34.14 E-value=42 Score=32.51 Aligned_cols=97 Identities=19% Similarity=0.354 Sum_probs=67.6
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHH--hhhccHHHHHHHHHhhcc--CCcHHHHHHHHHHHHHHHHH
Q psy6184 11 SHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIH--DEVGTKAFMEQMKELVRG--TQHEEVKAKILELIQAWAHA 86 (156)
Q Consensus 11 k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh--~eIask~Fl~~l~kl~~~--~~~~~Vk~kil~li~~Wa~~ 86 (156)
|..|.++-|-|+..-|.-=+-+|.|+|+.|...-.-|. .++-...|...+.+-+.+ ....+.|.+|+..+-.|...
T Consensus 41 khVVqsVeKfi~kCkpe~Kl~gLYVIDSIVRqsrhq~~~~kd~F~prf~~n~~~tf~~L~~c~~edks~iIrvlNlwqkn 120 (894)
T KOG0132|consen 41 KHVVQSVEKFIKKCKPEYKLPGLYVIDSIVRQSRHQFGKEKDVFGPRFSKNFTGTFQNLYECPQEDKSDIIRVLNLWQKN 120 (894)
T ss_pred HHHHHHHHHHHHhCCcccccCeeEEehHHHHHHHHhhcccccccCCccchhHHHHHHHHHhcCHHHHHHHHHhhhhhhcc
Confidence 45556666777777777778899999999987766555 233344566665554432 35567899999999999975
Q ss_pred --hhCCCCCcchH-HHHHhhhCCC-CCCC
Q psy6184 87 --FRNSPKYRAVP-TKSWMTDKGF-KNPS 111 (156)
Q Consensus 87 --F~~~~~l~~i~-~Y~~Lk~~Gi-~FP~ 111 (156)
|+. ..|. +.++-...|. .||.
T Consensus 121 ~VfK~----e~IqpLlDm~~~s~~~~~p~ 145 (894)
T KOG0132|consen 121 NVFKS----EIIQPLLDMADGSGLSVFPK 145 (894)
T ss_pred cchhH----HHHHHHHHHHhccCccccCC
Confidence 653 2477 8888888774 5665
No 99
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=33.40 E-value=1.4e+02 Score=20.04 Aligned_cols=34 Identities=12% Similarity=0.269 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCcchH-HHHHhhhCCCC
Q psy6184 72 VKAKILELIQAWAHAFRNSPKYRAVP-TKSWMTDKGFK 108 (156)
Q Consensus 72 Vk~kil~li~~Wa~~F~~~~~l~~i~-~Y~~Lk~~Gi~ 108 (156)
.++++.+|+..|...-..... +. +.+.|+.-|..
T Consensus 38 ~~eq~~~mL~~W~~k~G~~At---~~~L~~aL~~~~~~ 72 (79)
T cd08784 38 HRDRVYELLRIWRNKEGRKAT---LNTLIKALKDLDQR 72 (79)
T ss_pred hHHHHHHHHHHHHhccCcCcH---HHHHHHHHHHcccH
Confidence 899999999999987655433 66 88888877754
No 100
>PTZ00429 beta-adaptin; Provisional
Probab=33.36 E-value=2.9e+02 Score=26.63 Aligned_cols=27 Identities=22% Similarity=0.261 Sum_probs=22.6
Q ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHH
Q psy6184 10 PSHALASIKKKLTNSNPHIVLYALLVL 36 (156)
Q Consensus 10 ~k~AvraL~KrL~~~n~~v~l~AL~LL 36 (156)
+--|+..|+|=++++||.+.-+||..+
T Consensus 103 alLaINtl~KDl~d~Np~IRaLALRtL 129 (746)
T PTZ00429 103 ALLAVNTFLQDTTNSSPVVRALAVRTM 129 (746)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHH
Confidence 457899999999999999988888643
No 101
>smart00185 ARM Armadillo/beta-catenin-like repeats. Approx. 40 amino acid repeat. Tandem repeats form superhelix of helices that is proposed to mediate interaction of beta-catenin with its ligands. Involved in transducing the Wingless/Wnt signal. In plakoglobin arm repeats bind alpha-catenin and N-cadherin.
Probab=32.75 E-value=85 Score=17.06 Aligned_cols=27 Identities=19% Similarity=0.240 Sum_probs=20.9
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHH
Q psy6184 13 ALASIKKKLTNSNPHIVLYALLVLESC 39 (156)
Q Consensus 13 AvraL~KrL~~~n~~v~l~AL~LLe~~ 39 (156)
++..|.+-|.+.++.++..|+..|..+
T Consensus 13 ~i~~L~~ll~~~~~~i~~~a~~aL~nl 39 (41)
T smart00185 13 GLPALVELLKSEDEEVVKEAAWALSNL 39 (41)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 466677777888999999988877654
No 102
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=32.09 E-value=1.5e+02 Score=20.95 Aligned_cols=38 Identities=13% Similarity=0.327 Sum_probs=26.5
Q ss_pred cHHHHHHHHHHHHHHHHHhhCCCCCcchHHHHHhhhCCCC
Q psy6184 69 HEEVKAKILELIQAWAHAFRNSPKYRAVPTKSWMTDKGFK 108 (156)
Q Consensus 69 ~~~Vk~kil~li~~Wa~~F~~~~~l~~i~~Y~~Lk~~Gi~ 108 (156)
+...+++..+|++.|.........+.. +-..|+.-|..
T Consensus 45 ~~d~~Eq~~qmL~~W~~~~G~~a~~~~--Li~aLr~~~l~ 82 (97)
T cd08316 45 PQDTAEQKVQLLRAWYQSHGKTGAYRT--LIKTLRKAKLC 82 (97)
T ss_pred CCChHHHHHHHHHHHHHHhCCCchHHH--HHHHHHHccch
Confidence 345799999999999998876555322 44666665543
No 103
>PF05004 IFRD: Interferon-related developmental regulator (IFRD); InterPro: IPR007701 Interferon-related developmental regulator (IFRD1) is the human homologue of the Rattus norvegicus early response protein PC4 and its murine homologue TIS7 []. The exact function of IFRD1 is unknown but it has been shown that PC4 is necessary for muscle differentiation and that it might have a role in signal transduction. This entry also contains IFRD2 and its murine equivalent SKMc15, which are highly expressed soon after gastrulation and in the hepatic primordium, suggesting an involvement in early hematopoiesis [].
Probab=32.07 E-value=2.6e+02 Score=23.61 Aligned_cols=66 Identities=17% Similarity=0.126 Sum_probs=42.5
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccC-CcHHHHHHHHH
Q psy6184 13 ALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGT-QHEEVKAKILE 78 (156)
Q Consensus 13 AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~-~~~~Vk~kil~ 78 (156)
.+.++.|-|+.+.+.++.+|+.++..++-..|..-..+-.-+++...|..++.+. ....+|..++.
T Consensus 87 L~~~~~k~lkkg~~~E~~lA~~~l~Ll~ltlg~g~~~~ei~~~~~~~L~~~l~d~s~~~~~R~~~~~ 153 (309)
T PF05004_consen 87 LLDALLKSLKKGKSEEQALAARALALLALTLGAGEDSEEIFEELKPVLKRILTDSSASPKARAACLE 153 (309)
T ss_pred HHHHHHHHhccCCHHHHHHHHHHHHHHhhhcCCCccHHHHHHHHHHHHHHHHhCCccchHHHHHHHH
Confidence 4567778888888899999999999988886522222111245556666776653 33455555543
No 104
>cd08803 Death_ank3 Death domain of Ankyrin-3. Death Domain (DD) of the human protein ankyrin-3 (ANK-3) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-3, also called anykyrin-G (for general or giant), is found in neurons and at least one splice variant has been shown to be essential for propagation of action potentials as a binding partner to neurofascin and voltage-gated sodium channels. It is required for maintaining axo-dendritic polarity, and may be a genetic risk factor associated with bipolar disorder. ANK-3 may also play roles in other cell types. Mutations affecting ANK-3 pathways for Na channel localization are associated with Brugada syndrome, a potentially fata arrythmia. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by se
Probab=31.63 E-value=1.1e+02 Score=21.10 Aligned_cols=67 Identities=12% Similarity=0.106 Sum_probs=39.7
Q ss_pred HHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHHhhCCCCCcchH-HHHHhhhCC
Q psy6184 37 ESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAHAFRNSPKYRAVP-TKSWMTDKG 106 (156)
Q Consensus 37 e~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~F~~~~~l~~i~-~Y~~Lk~~G 106 (156)
..+..|-|.....-...=.|-..=+..++...+..+.+++..++..|......+.. +. +...|++=|
T Consensus 8 ~~ia~~LG~dW~~LA~eLg~s~~dI~~i~~e~p~~~~~q~~~lL~~W~~r~g~~At---~~~L~~aL~~i~ 75 (84)
T cd08803 8 AIVADHLGLSWTELARELNFSVDEINQIRVENPNSLIAQSFMLLKKWVTRDGKNAT---TDALTSVLTKIN 75 (84)
T ss_pred HHHHHHhhccHHHHHHHcCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHHhhCCCcH---HHHHHHHHHHCC
Confidence 34445666665543333344443333343322355999999999999988765544 55 666666544
No 105
>PF11707 Npa1: Ribosome 60S biogenesis N-terminal; InterPro: IPR021714 Npa1p is required for ribosome biogenesis and operates in the same functional environment as Rsa3p and Dbp6p during early maturation of 60S ribosomal subunits []. The protein partners of Npa1p include eight putative helicases as well as the novel Npa2p factor. Npa1p can also associate with a subset of H/ACA and C/D small nucleolar RNPs (snoRNPs) involved in the chemical modification of residues in the vicinity of the peptidyl transferase centre []. The protein has also been referred to as Urb1, and this domain at the N-terminal is one of several conserved regions along the length.
Probab=31.44 E-value=3.2e+02 Score=23.08 Aligned_cols=71 Identities=17% Similarity=0.173 Sum_probs=41.7
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHHccc---hhHHhhhccHHHHHHHHHhhccCC---cHHHHHHHHHHHHHHH
Q psy6184 14 LASIKKKLTNSNPHIVLYALLVLESCVKNCG---NLIHDEVGTKAFMEQMKELVRGTQ---HEEVKAKILELIQAWA 84 (156)
Q Consensus 14 vraL~KrL~~~n~~v~l~AL~LLe~~vkNCG---~~fh~eIask~Fl~~l~kl~~~~~---~~~Vk~kil~li~~Wa 84 (156)
+..|-|-|..-.+.++.+.|..|+..|-... +.....+-+..++..|..+..... ...|.+.+-+++..-.
T Consensus 160 ~~~l~k~l~~D~~~~v~~iL~~l~~~Vl~~~~v~r~~K~~~fn~~~L~~l~~Ly~~~~~~~~~~~~~~vh~fL~~lc 236 (330)
T PF11707_consen 160 MSALFKGLRKDPPETVILILETLKDKVLKDSSVSRSTKCKLFNEWTLSQLASLYSRDGEDEKSSVADLVHEFLLALC 236 (330)
T ss_pred HHHHHhcccCCCHHHHHHHHHHHHHHhccCCCCChhhhhhhcCHHHHHHHHHHhcccCCcccchHHHHHHHHHHHHh
Confidence 4556666666677788888888877665544 344555556666777777654321 1345555555444433
No 106
>COG1413 FOG: HEAT repeat [Energy production and conversion]
Probab=31.32 E-value=2.9e+02 Score=22.67 Aligned_cols=65 Identities=17% Similarity=0.249 Sum_probs=44.8
Q ss_pred CCChHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHH
Q psy6184 7 TIVPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAW 83 (156)
Q Consensus 7 ~~~~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~W 83 (156)
+.+.++++..|++.+...++.+...|.. --.++..+.=+..+++++.+..+..|+......+..-
T Consensus 69 ~~~~~~av~~l~~~l~d~~~~vr~~a~~------------aLg~~~~~~a~~~li~~l~~d~~~~vR~~aa~aL~~~ 133 (335)
T COG1413 69 ELGSEEAVPLLRELLSDEDPRVRDAAAD------------ALGELGDPEAVPPLVELLENDENEGVRAAAARALGKL 133 (335)
T ss_pred hhchHHHHHHHHHHhcCCCHHHHHHHHH------------HHHccCChhHHHHHHHHHHcCCcHhHHHHHHHHHHhc
Confidence 4567888888888888888877777776 1233455666777777776556677777766555443
No 107
>PF08711 Med26: TFIIS helical bundle-like domain; InterPro: IPR017923 Transcription factor IIS (TFIIS) is a transcription elongation factor that increases the overall transcription rate of RNA polymerase II by reactivating transcription elongation complexes that have arrested transcription. The three structural domains of TFIIS are conserved from yeast to human. The 80 or so N-terminal residues form a protein interaction domain containing a conserved motif, which has been called the LW motif because of the invariant leucine and tryptophan residues it contains. Although the N-terminal domain is not needed for transcriptional activity, a similar sequence has been identified in other transcription factors and proteins that are predominantly nuclear localized [, ]: MED26 (also known as CRSP70 and ARC70), a subunit of the Mediator complex, which is required for the activity of the enhancer-binding protein Sp1. Elongin A, a subunit of a transcription elongation factor previously known as SIII. It increases the rate of transcription by suppressing transient pausing of the elongation complex. PPP1R10, a nuclear regulatory subunit of protein phosphatase 1 that was previously known as p99, FB19 or PNUTS. PIBP, a small hypothetical protein that could be a phosphoinositide binding protein. IWS1, which is thought to function in both transcription initiation and elongation. The TFIIS N-terminal domain is a compact four-helix bundle. The hydrophobic core residues of helices 2, 3, and 4 are well conserved among TFIIS domains, although helix 1 is less conserved []. ; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 1EO0_A 3OAK_A 3NFQ_B 3O8Z_A 1WJT_A 2XPL_A 2XPO_A 2XPP_A 2XPN_A.
Probab=30.75 E-value=1.1e+02 Score=18.56 Aligned_cols=20 Identities=25% Similarity=0.571 Sum_probs=16.8
Q ss_pred CCcHHHHHHHHHHHHHHHHH
Q psy6184 67 TQHEEVKAKILELIQAWAHA 86 (156)
Q Consensus 67 ~~~~~Vk~kil~li~~Wa~~ 86 (156)
..+.+|++.+..++..|...
T Consensus 32 ~~~~~i~~~A~~Li~~Wk~~ 51 (53)
T PF08711_consen 32 SENPEIRKLAKELIKKWKRI 51 (53)
T ss_dssp TS-HHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHhHh
Confidence 37899999999999999864
No 108
>KOG2075|consensus
Probab=30.73 E-value=1.9e+02 Score=26.73 Aligned_cols=78 Identities=18% Similarity=0.364 Sum_probs=55.3
Q ss_pred hHHHHHHHHHHhcCCCHHHHHHH-------HHHHHHHHHccchhHHhhhccHHH------HHHHHHhhccCCcHHHHHHH
Q psy6184 10 PSHALASIKKKLTNSNPHIVLYA-------LLVLESCVKNCGNLIHDEVGTKAF------MEQMKELVRGTQHEEVKAKI 76 (156)
Q Consensus 10 ~k~AvraL~KrL~~~n~~v~l~A-------L~LLe~~vkNCG~~fh~eIask~F------l~~l~kl~~~~~~~~Vk~ki 76 (156)
.++||+.|++++.-.|.=.-+.+ =.|+..|++.-...|-..+....| .+.+..++...+-..=.-++
T Consensus 206 er~CVkflr~~l~~~naf~~L~q~A~lf~ep~Li~~c~e~id~~~~~al~~EGf~did~~~dt~~evl~r~~l~~~e~~l 285 (521)
T KOG2075|consen 206 ERQCVKFLRKNLMADNAFLELFQRAKLFDEPSLISICLEVIDKSFEDALTPEGFCDIDSTRDTYEEVLRRDTLEAREFRL 285 (521)
T ss_pred HHHHHHHHHHhcCChHHHHHHHHHHHhhcCHHHHHHHHHHhhhHHHhhhCccceeehhhHHHHHHHHHhhcccchhHHHH
Confidence 47899999999988776666555 156777877777777776665544 45566677654443336789
Q ss_pred HHHHHHHHHHh
Q psy6184 77 LELIQAWAHAF 87 (156)
Q Consensus 77 l~li~~Wa~~F 87 (156)
.+....|+..=
T Consensus 286 feA~lkw~~~e 296 (521)
T KOG2075|consen 286 FEAALKWAEAE 296 (521)
T ss_pred HHHHHhhccCc
Confidence 99999999753
No 109
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.54 E-value=2.4e+02 Score=27.33 Aligned_cols=57 Identities=21% Similarity=0.395 Sum_probs=40.7
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhcc-CCcHHHHHHHHHHHHHHHHHhhCCC
Q psy6184 15 ASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRG-TQHEEVKAKILELIQAWAHAFRNSP 91 (156)
Q Consensus 15 raL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~-~~~~~Vk~kil~li~~Wa~~F~~~~ 91 (156)
+.|.|||-++++.-+--=+.++..+=+=| ..+|+..+.+++.+ +.+ ++.+++|++.|
T Consensus 468 ~~laKRLL~g~S~s~~~E~~mis~LKk~~---------g~~fT~Kle~Mf~DIsLS-----------~e~~~af~~s~ 525 (773)
T COG5647 468 KLLAKRLLNGRSASAQAELKMISMLKKVC---------GQEFTSKLEGMFRDISLS-----------SEFTEAFQHSP 525 (773)
T ss_pred HHHHHHHhcCCCcchHHHHHHHHHHHHHh---------hhHHHHHHHHHHHhcchh-----------HHHHHHHhhCc
Confidence 46778888887766666777777775544 56788888888865 222 67778888766
No 110
>KOG0151|consensus
Probab=30.43 E-value=2.1e+02 Score=27.85 Aligned_cols=81 Identities=14% Similarity=0.300 Sum_probs=52.5
Q ss_pred CChHHHHHHHHHHhcCCCHH--HHHHHHHHHHHHHHccchhHHhhhccH-HHHHHHHHhhcc-----------CCcHHHH
Q psy6184 8 IVPSHALASIKKKLTNSNPH--IVLYALLVLESCVKNCGNLIHDEVGTK-AFMEQMKELVRG-----------TQHEEVK 73 (156)
Q Consensus 8 ~~~k~AvraL~KrL~~~n~~--v~l~AL~LLe~~vkNCG~~fh~eIask-~Fl~~l~kl~~~-----------~~~~~Vk 73 (156)
+++-|.+.+|.+-|...++- .=+.=|.|+.-..-||-.++....+=+ .|-..|.+|+.+ -+.+..|
T Consensus 462 ~aa~EI~eci~eSlt~~~t~~~kKiarLyLvsDIL~N~sarv~nas~YR~~FEa~L~~Ifd~l~~~yr~I~gRIkaE~fk 541 (877)
T KOG0151|consen 462 DAAGEIVECITESLTNKETPLPKKIARLYLVSDILHNSSARVANASAYRKSFEATLEDIFDDLNDLYRSIGGRIKAEAFK 541 (877)
T ss_pred hhHHHHHHHHHHHHhccCCcchhHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHH
Confidence 45667788888888654322 222335677778889988755544433 333335555431 1346789
Q ss_pred HHHHHHHHHHHHHhh
Q psy6184 74 AKILELIQAWAHAFR 88 (156)
Q Consensus 74 ~kil~li~~Wa~~F~ 88 (156)
+|++..|+.|.+.|-
T Consensus 542 qRV~kVirvWedW~i 556 (877)
T KOG0151|consen 542 QRVMKVIRVWEDWAI 556 (877)
T ss_pred HHHHHHHHHHHHHHh
Confidence 999999999999876
No 111
>PF10508 Proteasom_PSMB: Proteasome non-ATPase 26S subunit; InterPro: IPR019538 The 26S proteasome is an enzymatic complex that degrades ubiquitinated proteins in eukaryotic cells. 26S proteasome non-ATPase regulatory subunit 5 is one of a number of chaperones that are involved in the assembly of the proteasome. The chaperones dissociate before 26S proteasome formation is complete [].; GO: 0044183 protein binding involved in protein folding
Probab=28.96 E-value=3.8e+02 Score=24.14 Aligned_cols=67 Identities=13% Similarity=0.154 Sum_probs=44.0
Q ss_pred HHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHH
Q psy6184 17 IKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAH 85 (156)
Q Consensus 17 L~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~ 85 (156)
|..-+.+.|..+.++.+.++-.+.+.....+.. +.+..+++.+.+-+++ .|.-|+--+++++...+.
T Consensus 165 L~~l~~~~~~~vR~Rv~el~v~i~~~S~~~~~~-~~~sgll~~ll~eL~~-dDiLvqlnalell~~La~ 231 (503)
T PF10508_consen 165 LKSLMSQSSDIVRCRVYELLVEIASHSPEAAEA-VVNSGLLDLLLKELDS-DDILVQLNALELLSELAE 231 (503)
T ss_pred HHHHHhccCHHHHHHHHHHHHHHHhcCHHHHHH-HHhccHHHHHHHHhcC-ccHHHHHHHHHHHHHHHc
Confidence 333344445666666666555555554444433 3345688888887776 678899999999999987
No 112
>COG5181 HSH155 U2 snRNP spliceosome subunit [RNA processing and modification]
Probab=28.84 E-value=76 Score=30.50 Aligned_cols=35 Identities=26% Similarity=0.429 Sum_probs=29.1
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHH---HHHccchh
Q psy6184 12 HALASIKKKLTNSNPHIVLYALLVLES---CVKNCGNL 46 (156)
Q Consensus 12 ~AvraL~KrL~~~n~~v~l~AL~LLe~---~vkNCG~~ 46 (156)
-.+-.|.++|+|+.|++-.+|+.+.-+ ..||||+.
T Consensus 604 ~ivStiL~~L~~k~p~vR~~aadl~~sl~~vlk~c~e~ 641 (975)
T COG5181 604 MIVSTILKLLRSKPPDVRIRAADLMGSLAKVLKACGET 641 (975)
T ss_pred HHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHhcchH
Confidence 346778999999999999999987666 56899985
No 113
>PF04123 DUF373: Domain of unknown function (DUF373); InterPro: IPR007254 This archaeal family of unknown function is predicted to be an integral membrane protein with six transmembrane regions.
Probab=28.11 E-value=53 Score=28.64 Aligned_cols=36 Identities=17% Similarity=0.103 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHHHhhCCCCC----cchHHHHHhhhCCCC
Q psy6184 73 KAKILELIQAWAHAFRNSPKY----RAVPTKSWMTDKGFK 108 (156)
Q Consensus 73 k~kil~li~~Wa~~F~~~~~l----~~i~~Y~~Lk~~Gi~ 108 (156)
++.+++.....+.+=+.|++. ..+++|++||++|.+
T Consensus 27 re~vl~AA~~l~laDPeDSD~N~if~avkiydeL~~~Ged 66 (344)
T PF04123_consen 27 REAVLDAAVKLALADPEDSDVNAIFGAVKIYDELKAEGED 66 (344)
T ss_pred HHHHHHHHHHHhcCCcccccHHHHHHHHHHHHHHHhcCCC
Confidence 788888888888887888874 444599999999974
No 114
>TIGR01802 CM_pl-yst monofunctional chorismate mutase, eukaryotic type. This model represents the plant and yeast (plastidic) chorismate mutase. These CM's are distinct from other forms by the presence of an extended regulatory domain.
Probab=28.05 E-value=3.4e+02 Score=22.68 Aligned_cols=25 Identities=28% Similarity=0.388 Sum_probs=22.1
Q ss_pred CcHHHHHHHHHHHHHHHHHhhCCCC
Q psy6184 68 QHEEVKAKILELIQAWAHAFRNSPK 92 (156)
Q Consensus 68 ~~~~Vk~kil~li~~Wa~~F~~~~~ 92 (156)
|...|-++|++-+..=|..|..||.
T Consensus 183 T~~aVE~~Vl~Rv~~KA~~yGqd~~ 207 (246)
T TIGR01802 183 TDPAVEEKILERLAKKARVYGVDPT 207 (246)
T ss_pred hhHHHHHHHHHHHHHHHHhhCCCCC
Confidence 6788999999999999999988775
No 115
>KOG2160|consensus
Probab=27.77 E-value=4e+02 Score=23.32 Aligned_cols=78 Identities=18% Similarity=0.270 Sum_probs=51.9
Q ss_pred HHHHHHHHhcCCCHHHH-HHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhcc-CCcHHHHHHHHHHHHHHHHHhhCC
Q psy6184 13 ALASIKKKLTNSNPHIV-LYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRG-TQHEEVKAKILELIQAWAHAFRNS 90 (156)
Q Consensus 13 AvraL~KrL~~~n~~v~-l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~-~~~~~Vk~kil~li~~Wa~~F~~~ 90 (156)
+.+.|.+.+.+.+|+.+ -.||--+-++++|--.....-..-.. ...|+.++.+ .++...|.|++.|+.....+=+.+
T Consensus 167 ~L~~Ll~~ls~~~~~~~r~kaL~AissLIRn~~~g~~~fl~~~G-~~~L~~vl~~~~~~~~lkrK~~~Ll~~Ll~~~~s~ 245 (342)
T KOG2160|consen 167 ALSKLLKILSSDDPNTVRTKALFAISSLIRNNKPGQDEFLKLNG-YQVLRDVLQSNNTSVKLKRKALFLLSLLLQEDKSD 245 (342)
T ss_pred cHHHHHHHHccCCCchHHHHHHHHHHHHHhcCcHHHHHHHhcCC-HHHHHHHHHcCCcchHHHHHHHHHHHHHHHhhhhh
Confidence 56777777766555544 77777777888886554322222222 4456666654 478899999999999998875544
Q ss_pred C
Q psy6184 91 P 91 (156)
Q Consensus 91 ~ 91 (156)
.
T Consensus 246 ~ 246 (342)
T KOG2160|consen 246 E 246 (342)
T ss_pred h
Confidence 3
No 116
>PF11264 ThylakoidFormat: Thylakoid formation protein; InterPro: IPR017499 Psp29, originally designated sll1414 (P73956 from SWISSPROT) in Synechocystis sp. (strain PCC 6803), is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.; GO: 0010027 thylakoid membrane organization, 0015979 photosynthesis, 0009523 photosystem II
Probab=27.49 E-value=13 Score=30.43 Aligned_cols=64 Identities=17% Similarity=0.320 Sum_probs=36.6
Q ss_pred HHHHHHHHHhhccCCcHHHHHHHHHH-HHHHHHHhhCCCCCcc-hH-HHHHhhhCCCCCCCCCCCCCCC
Q psy6184 54 KAFMEQMKELVRGTQHEEVKAKILEL-IQAWAHAFRNSPKYRA-VP-TKSWMTDKGFKNPSKSSDSLGL 119 (156)
Q Consensus 54 k~Fl~~l~kl~~~~~~~~Vk~kil~l-i~~Wa~~F~~~~~l~~-i~-~Y~~Lk~~Gi~FP~~~~~a~f~ 119 (156)
+.|....-..|..-...-|.+.+.++ +......|..||=|.. ++ +|+.+-. ||+ |+.+.+++|.
T Consensus 7 r~F~~~~~~pI~siYrrvv~ELLVe~HLl~~n~~F~yD~lfalG~vt~fd~fm~-GY~-p~~~~~~If~ 73 (216)
T PF11264_consen 7 RAFYKAFPRPIPSIYRRVVDELLVELHLLSVNKDFQYDPLFALGLVTVFDRFMQ-GYP-PEEDKDSIFN 73 (216)
T ss_pred HHHHHhCCCCCcHHHHHHHHHHHHHHHHHHhccCceeCchHHhhHHHHHHHHhc-CCC-ChhHHHHHHH
Confidence 34444444333322223344444444 5556668888887754 66 8888864 886 6666666543
No 117
>PLN02344 chorismate mutase
Probab=27.33 E-value=3.4e+02 Score=23.20 Aligned_cols=26 Identities=15% Similarity=0.225 Sum_probs=22.3
Q ss_pred CcHHHHHHHHHHHHHHHHHhhCCCCC
Q psy6184 68 QHEEVKAKILELIQAWAHAFRNSPKY 93 (156)
Q Consensus 68 ~~~~Vk~kil~li~~Wa~~F~~~~~l 93 (156)
|...|-++|++-+..=|..|..||.+
T Consensus 216 T~~aVE~~Vl~Rv~~KA~~yGqd~~~ 241 (284)
T PLN02344 216 TFEAVEEAVKKRVEKKARTFGQEVTL 241 (284)
T ss_pred hhHHHHHHHHHHHHHHHHhhCCCCCC
Confidence 67889999999999999999887753
No 118
>PF11882 DUF3402: Domain of unknown function (DUF3402); InterPro: IPR021819 This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is typically between 350 to 473 amino acids in length. This domain is found associated with PF07923 from PFAM.
Probab=27.31 E-value=90 Score=27.74 Aligned_cols=34 Identities=38% Similarity=0.551 Sum_probs=30.1
Q ss_pred HHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHh
Q psy6184 16 SIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHD 49 (156)
Q Consensus 16 aL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~ 49 (156)
.|||=|+-++|..++++|.|+-.+|.=||....+
T Consensus 298 iLKk~l~v~~~~l~ly~LKl~K~qvPy~GRKWr~ 331 (409)
T PF11882_consen 298 ILKKILKVPNPMLQLYILKLLKSQVPYCGRKWRQ 331 (409)
T ss_pred HHHHHHcCCChHHHHHHHHHHHHhcccccchhhh
Confidence 4555568899999999999999999999999866
No 119
>PLN03076 ARF guanine nucleotide exchange factor (ARF-GEF); Provisional
Probab=27.26 E-value=1.9e+02 Score=30.71 Aligned_cols=58 Identities=17% Similarity=0.312 Sum_probs=37.6
Q ss_pred cCCCHHHHHHHHHHHHHHHHccchhHHhhhcc----HHHHHHHHHhhccCCcHHHHHHHHHHHH
Q psy6184 22 TNSNPHIVLYALLVLESCVKNCGNLIHDEVGT----KAFMEQMKELVRGTQHEEVKAKILELIQ 81 (156)
Q Consensus 22 ~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIas----k~Fl~~l~kl~~~~~~~~Vk~kil~li~ 81 (156)
-|+|.++.++|+..|.-+.--.-+ ..|+.. ++||+-+..++.+..+.+||+.|++.+.
T Consensus 1147 ~~~n~~va~fAidsLrQLs~kfle--~eEL~~f~FQkefLkPfe~im~~s~~~eVrE~ILeCv~ 1208 (1780)
T PLN03076 1147 CSENLSIAIFAMDSLRQLSMKFLE--REELANYNFQNEFMKPFVIVMRKSNAVEIRELIIRCVS 1208 (1780)
T ss_pred CCcchhHHHHHHHHHHHHHHHhcc--hhhhhchhHHHHHHHHHHHHHHhcCchHHHHHHHHHHH
Confidence 366888878887765443222211 112222 5777778888877778899999998775
No 120
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=27.08 E-value=1.6e+02 Score=20.61 Aligned_cols=33 Identities=9% Similarity=0.341 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHHhhCCCCCcchH-HHHHhhhCCCC
Q psy6184 73 KAKILELIQAWAHAFRNSPKYRAVP-TKSWMTDKGFK 108 (156)
Q Consensus 73 k~kil~li~~Wa~~F~~~~~l~~i~-~Y~~Lk~~Gi~ 108 (156)
++++.+|+..|...-..... +. +...|+.-|..
T Consensus 47 ~eq~~qmL~~W~~~~G~~At---~~~L~~aL~~~~~~ 80 (96)
T cd08315 47 REQLYQMLLTWVNKTGRKAS---VNTLLDALEAIGLR 80 (96)
T ss_pred HHHHHHHHHHHHHhhCCCcH---HHHHHHHHHHcccc
Confidence 99999999999988665444 66 77777776654
No 121
>PF02854 MIF4G: MIF4G domain; InterPro: IPR003890 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 3", and is found in nuclear cap-binding proteins, eIF4G, and UPF2. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA. Nonsense-mediated mRNA decay (NMD) in eukaryotes involves UPF1, UPF2 and UPF3 to accelerate the decay rate of two unique classes of transcripts: (1) nonsense mRNAs that arise through errors in gene expression, and (2) naturally occurring transcripts that lack coding errors but have built-in features that target them for accelerated decay (error-free mRNAs). NMD can trigger decay during any round of translation and can target CBC-bound or eIF-4E-bound transcripts []. UPF2 contains MIF4G domains, while UPF3 contains an RNP domain []. ; GO: 0005515 protein binding, 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A 1HU3_A 3RK6_A ....
Probab=26.80 E-value=2.6e+02 Score=20.57 Aligned_cols=55 Identities=11% Similarity=0.197 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHH----Hhhc----cCCcHHHHHHHHHHHH
Q psy6184 27 HIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMK----ELVR----GTQHEEVKAKILELIQ 81 (156)
Q Consensus 27 ~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~----kl~~----~~~~~~Vk~kil~li~ 81 (156)
......+.++=.+.++||..+...=.++..++++. ..+. ...+..++-.+.+++.
T Consensus 142 ~~~~~~ie~~~~lL~~~G~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~r~~~~l~~l~~ 204 (209)
T PF02854_consen 142 PPDEENIECLCTLLKTCGKKLENSEESPKALDEIFERLQKYANSKKDPNLSSRIRFMLEDLIE 204 (209)
T ss_dssp HTCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCHSSSSSHHHHHHHHHHHH
T ss_pred CCcHhHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHHHH
Confidence 44455666677778888999882223444555544 3332 2456777777776664
No 122
>COG5209 RCD1 Uncharacterized protein involved in cell differentiation/sexual development [General function prediction only]
Probab=26.61 E-value=1.3e+02 Score=25.46 Aligned_cols=38 Identities=18% Similarity=0.152 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhc
Q psy6184 28 IVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVR 65 (156)
Q Consensus 28 v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~ 65 (156)
.-+-||-++.++|||...-+|...-+-+.+--+.++..
T Consensus 162 LRltsLGVIgaLvkNdsq~vi~fLltTeivPLcLrIme 199 (315)
T COG5209 162 LRLTSLGVIGALVKNDSQYVIKFLLTTEIVPLCLRIME 199 (315)
T ss_pred eeehHHHHHHHHHhCCCHHHHHHHHhhhHHHHHHHHHH
Confidence 44668999999999999999988877766666566654
No 123
>cd08324 CARD_NOD1_CARD4 Caspase activation and recruitment domain similar to that found in NOD1. Caspase activation and recruitment domain (CARD) found in human NOD1 (CARD4) and similar proteins. NOD1 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD1, as well as NOD2, the N-terminal effector domain is a CARD. Nod1-CARD has been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form hom
Probab=25.95 E-value=1.7e+02 Score=20.52 Aligned_cols=26 Identities=19% Similarity=0.236 Sum_probs=18.4
Q ss_pred HhhccCCcHHHHHHHHHHHHHHHHHh
Q psy6184 62 ELVRGTQHEEVKAKILELIQAWAHAF 87 (156)
Q Consensus 62 kl~~~~~~~~Vk~kil~li~~Wa~~F 87 (156)
.+....|+.+=.++++.+++.|++.-
T Consensus 37 ~V~a~~T~qdkmRkLld~v~akG~~~ 62 (85)
T cd08324 37 IVCACPTQPDKVRKILDLVQSKGEEV 62 (85)
T ss_pred HHHhCCCCHHHHHHHHHHHHhcCchH
Confidence 33445677777788888899888653
No 124
>KOG3219|consensus
Probab=25.61 E-value=1.5e+02 Score=23.85 Aligned_cols=46 Identities=17% Similarity=0.243 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCc-chH-HHHHhhhCCCCCCCCCCCCCC
Q psy6184 70 EEVKAKILELIQAWAHAFRNSPKYR-AVP-TKSWMTDKGFKNPSKSSDSLG 118 (156)
Q Consensus 70 ~~Vk~kil~li~~Wa~~F~~~~~l~-~i~-~Y~~Lk~~Gi~FP~~~~~a~f 118 (156)
-+|.+-++.+-..|.+ +.|=.+ .|+ +|..|+.+|--++..---.||
T Consensus 147 GEvVEeAl~V~~~~~e---~~PLqP~HIREA~rrL~~qgk~~~~~~~~~~f 194 (195)
T KOG3219|consen 147 GEVVEEALDVREEWGE---SGPLQPKHIREAYRRLKLQGKLPNSRYKKSMF 194 (195)
T ss_pred HHHHHHHHHHHHHhcc---CCCCCcHHHHHHHHHHHhcCCCCCCccccccc
Confidence 4678889999999997 333333 488 999999999765343333343
No 125
>PF12993 DUF3877: Domain of unknown function, E. rectale Gene description (DUF3877); InterPro: IPR024539 This entry represents proteins of unknown function found primarily in Firmicutes. The Eubacterium rectale gene appears to be upregulated in the presence of Bacteroides thetaiotaomicron compared to growth in pure culture [].
Probab=25.22 E-value=61 Score=25.69 Aligned_cols=40 Identities=25% Similarity=0.483 Sum_probs=32.5
Q ss_pred HHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHHhh
Q psy6184 47 IHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAHAFR 88 (156)
Q Consensus 47 fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~F~ 88 (156)
+|.++...+|+.+++.++.+ +.--.+.|++++..|++...
T Consensus 87 Vhe~~~~~eFik~lIe~v~~--hgcT~e~I~~~F~~ys~~~~ 126 (175)
T PF12993_consen 87 VHEHTKENEFIKELIELVGK--HGCTLEDILELFHKYSDNVH 126 (175)
T ss_pred HHhcCCCCHHHHHHHHHHhc--CCcCHHHHHHHHHHhcCCeE
Confidence 57888889999999999975 33457889999999987654
No 126
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=24.38 E-value=64 Score=16.52 Aligned_cols=18 Identities=11% Similarity=0.125 Sum_probs=13.1
Q ss_pred CCCcchH-HHHHhhhCCCC
Q psy6184 91 PKYRAVP-TKSWMTDKGFK 108 (156)
Q Consensus 91 ~~l~~i~-~Y~~Lk~~Gi~ 108 (156)
.++.... +|+.++++|+.
T Consensus 14 ~~~~~a~~~~~~M~~~g~~ 32 (35)
T TIGR00756 14 GRVEEALELFKEMLERGIE 32 (35)
T ss_pred CCHHHHHHHHHHHHHcCCC
Confidence 3444556 89999999985
No 127
>PF08045 CDC14: Cell division control protein 14, SIN component; InterPro: IPR012535 Cdc14 is a component of the septation initiation network (SIN) and is required for the localisation and activity of Sid1. Sid1 is a protein kinase that localises asymmetrically to one spindle pole body (SPB) in anaphase disappears prior to cell separation [], [].
Probab=24.31 E-value=4.2e+02 Score=22.12 Aligned_cols=72 Identities=14% Similarity=0.166 Sum_probs=43.6
Q ss_pred HHHHHHHHh-cCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhcc-CCcHHHHHHHHHHHHHHHH
Q psy6184 13 ALASIKKKL-TNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRG-TQHEEVKAKILELIQAWAH 85 (156)
Q Consensus 13 AvraL~KrL-~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~-~~~~~Vk~kil~li~~Wa~ 85 (156)
+++.|..=| ....+.++..+|..|-.++-.+...... +-.-+=+..+..++++ +++.+||-|+++.+.-|=.
T Consensus 134 ~m~lll~LL~~~~~~~i~~a~L~tLv~iLld~p~N~r~-FE~~~Gl~~v~~llk~~~~~~~~r~K~~EFL~fyl~ 207 (257)
T PF08045_consen 134 NMELLLDLLSPSNPPAIQSACLDTLVCILLDSPENQRD-FEELNGLSTVCSLLKSKSTDRELRLKCIEFLYFYLM 207 (257)
T ss_pred hHHHHHHHhccCCCchHHHHHHHHHHHHHHcChHHHHH-HHHhCCHHHHHHHHccccccHHHhHHHHHHHHHHHc
Confidence 455555555 3456788888887666655555444221 1111113445566654 6889999999999876643
No 128
>cd08051 gp6_gp15_like Head-Tail Connector Proteins gp6 and gp15, and similar proteins. Members of this family include the proteins gp6 and gp15 from bacteriophage HK97 and SPP1, respectively. They are critical in the assembly of the connector, a specialized structure that serves as an interface for head and tail attachment, as well as a point at which DNA exits the head during infection by the bacteriophage. They form dodecameric ring structures that comprise the middle ring of the connector, located between the portal protein (attached to the head) and the gp7/gp16 ring (attached to the tail). They are components of the mature phage and the absence or mutation of HK97 gp6 or SPP1 gp15, respectively, result in defective head-tail joining and the absence of mature phage particles. The genome maps of HK97 and SPP1 show that genes encoding gp6 and gp15 are in the same relative position on the genome, located adjacent to the major capsid protein (MCP) gene and in between head and tail gene
Probab=23.93 E-value=2.6e+02 Score=19.48 Aligned_cols=50 Identities=22% Similarity=0.418 Sum_probs=36.8
Q ss_pred CCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHH
Q psy6184 24 SNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAHA 86 (156)
Q Consensus 24 ~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~ 86 (156)
.+.-.+.+.....+.|-.-||.+|-..- ....+..||.-++.+++-|++.
T Consensus 14 dD~lL~~~i~aA~~~~e~~~~~~~~~~~-------------~~~lp~~vk~A~l~li~~~yen 63 (94)
T cd08051 14 RDELLTLYAQAAFDYCXRWCDEPFWDAV-------------AADIPAAVKGAVLKVFQFYFEH 63 (94)
T ss_pred CHHHHHHHHHHHHHHHHHHhcccccccc-------------ccCCCHHHHHHHHHHHHHHHHH
Confidence 3455666777888888888887754421 1246789999999999999764
No 129
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=23.82 E-value=2.3e+02 Score=24.12 Aligned_cols=24 Identities=13% Similarity=0.410 Sum_probs=21.1
Q ss_pred cCCcHHHHHHHHHHHHHHHHHhhC
Q psy6184 66 GTQHEEVKAKILELIQAWAHAFRN 89 (156)
Q Consensus 66 ~~~~~~Vk~kil~li~~Wa~~F~~ 89 (156)
.+++.+|+..+.+||..|...+..
T Consensus 54 kh~~~~I~~lAk~li~~WK~~v~~ 77 (299)
T TIGR01385 54 KHPNEDISKLAKKIIKSWKKVVDK 77 (299)
T ss_pred cCCcHHHHHHHHHHHHHHHHHHhh
Confidence 457789999999999999998875
No 130
>PF11698 V-ATPase_H_C: V-ATPase subunit H; InterPro: IPR011987 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. This entry represents the C-terminal domain of subunit H (also known as Vma13p) found in the V1 complex of V-ATPases. This subunit has a regulatory function, being responsible for activating ATPase activity and coupling ATPase activity to proton flow []. The yeast enzyme contains five motifs similar to the HEAT or Armadillo repeats seen in the importins, and can be divided into two distinct domains: a large N-terminal domain consisting of stacked alpha helices, and a smaller C-terminal alpha-helical domain with a similar superhelical topology to an armadillo repeat []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0015991 ATP hydrolysis coupled proton transport, 0000221 vacuolar proton-transporting V-type ATPase, V1 domain; PDB: 1HO8_A.
Probab=23.72 E-value=1.6e+02 Score=21.75 Aligned_cols=22 Identities=23% Similarity=0.449 Sum_probs=18.2
Q ss_pred hcCCCHHHHHHHHHHHHHHHHc
Q psy6184 21 LTNSNPHIVLYALLVLESCVKN 42 (156)
Q Consensus 21 L~~~n~~v~l~AL~LLe~~vkN 42 (156)
+.|.|+.|...||.-+..+|-|
T Consensus 95 m~h~d~eVr~eAL~avQklm~~ 116 (119)
T PF11698_consen 95 MNHEDPEVRYEALLAVQKLMVN 116 (119)
T ss_dssp TS-SSHHHHHHHHHHHHHHHHH
T ss_pred hcCCCHHHHHHHHHHHHHHHHh
Confidence 4799999999999998888765
No 131
>PF14726 RTTN_N: Rotatin, an armadillo repeat protein, centriole functioning
Probab=23.49 E-value=2.8e+02 Score=19.69 Aligned_cols=56 Identities=14% Similarity=0.151 Sum_probs=43.5
Q ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHcc-chhHHhhhccHHHHHHHHHhhc
Q psy6184 10 PSHALASIKKKLTNSNPHIVLYALLVLESCVKNC-GNLIHDEVGTKAFMEQMKELVR 65 (156)
Q Consensus 10 ~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNC-G~~fh~eIask~Fl~~l~kl~~ 65 (156)
++.-++.|-.=+++..+-..-.+|.++.-+++.- |...-..++..+|+.++.+.+.
T Consensus 28 ~~~Ll~~LleWFnf~~~~~~~~VL~Ll~~L~~~~~a~~~l~~iG~~~fL~klr~~~~ 84 (98)
T PF14726_consen 28 ERLLLKQLLEWFNFPPVPMKEEVLALLLRLLKSPYAAQILRDIGAVRFLSKLRPNVE 84 (98)
T ss_pred HHHHHHHHHHHhCCCCCccHHHHHHHHHHHHhCcHHHHHHHHccHHHHHHHHHhcCC
Confidence 4455555555566766668888999999999998 8888899999999888886553
No 132
>PF08951 EntA_Immun: Enterocin A Immunity; InterPro: IPR015046 Gram-positive lactobacilli produce bacteriocins to kill closely-related competitor species []. To protect themselves from the bacteriocidal activity of this molecule they co-express an immunity protein (for discussion of this operon see Bacteriocin_IIc PF10439 from PFAM). The immunity protein structure is a soluble, cytoplasmic, antiparallel four alpha-helical globular bundle with a fifth, more flexible and more divergent C-terminal helical hair-pin []. The C-terminal hair-pin recognises the C terminus of the producer bacteriocin and this interaction is sufficient to dis-orient the bacteriocin within the membrane and close up the permeabilising pore that on its own the bacteriocin creates []. These immunity proteins interact in the same way with other bacteriocins, family Bacteriocin_II, PF01721 from PFAM. Since many enterococci can produce more than one bacteriocin it seems likely that the whole operon can be carried on transferable plasmids []. ; PDB: 2BL8_C 2BL7_A 2K19_A 2FU2_A 1TDP_A 2IP6_A.
Probab=22.93 E-value=1.9e+02 Score=18.26 Aligned_cols=49 Identities=4% Similarity=0.133 Sum_probs=29.2
Q ss_pred HHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHHhhCCCCCcchH--HHHHhh
Q psy6184 54 KAFMEQMKELVRGTQHEEVKAKILELIQAWAHAFRNSPKYRAVP--TKSWMT 103 (156)
Q Consensus 54 k~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~F~~~~~l~~i~--~Y~~Lk 103 (156)
.+|++.|..++ +..+......+.+++......+.....+..+. ++..|.
T Consensus 4 ~~l~~~i~~l~-~~~~~~~~~~lr~iL~~a~~~l~~~~~~~~v~~~L~~~l~ 54 (75)
T PF08951_consen 4 EELLNIIYNLY-NDLDVKINEELRKILLKAKNELEKGENVPLVASRLNNDLS 54 (75)
T ss_dssp HHHHHHHHHHH-CCHCHHCGHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHH-hcccccCCHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHH
Confidence 46777777777 33344455566667777777777655544432 555444
No 133
>PF10762 DUF2583: Protein of unknown function (DUF2583) ; InterPro: IPR019698 Some members in this entry are annotated as YchH however currently no function is known.
Probab=22.82 E-value=41 Score=23.70 Aligned_cols=18 Identities=33% Similarity=0.892 Sum_probs=14.0
Q ss_pred ccCCccccccCcchHHHHHhhh
Q psy6184 133 EIKGIDQIVDSSSSVALWLRHF 154 (156)
Q Consensus 133 ~~~~~~q~~~~~~~~~~~~~~~ 154 (156)
-+.|+||++|- --|+|||
T Consensus 62 RigGrE~VaDR----YwWvkh~ 79 (89)
T PF10762_consen 62 RIGGREKVADR----YWWVKHF 79 (89)
T ss_pred cccCcchhhhh----HHHHHhh
Confidence 47888988874 5788887
No 134
>PF12074 DUF3554: Domain of unknown function (DUF3554); InterPro: IPR022716 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 287 to 356 amino acids in length. This domain is found associated with PF02985 from PFAM.
Probab=22.80 E-value=3.7e+02 Score=22.53 Aligned_cols=83 Identities=10% Similarity=0.128 Sum_probs=56.9
Q ss_pred CCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhc-cCCcHHHHHHHHHHHHHHHHHhhCCCCCcchH-HHHH
Q psy6184 24 SNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVR-GTQHEEVKAKILELIQAWAHAFRNSPKYRAVP-TKSW 101 (156)
Q Consensus 24 ~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~-~~~~~~Vk~kil~li~~Wa~~F~~~~~l~~i~-~Y~~ 101 (156)
..+....-.+.+|+++..+.....-.+. ...+-..++-++- ..++.+||+..+..+..+...-+..-....+. +++.
T Consensus 174 ~~~~d~~w~~~al~~~~~~~~~~~~~~~-~~~~~~a~i~ll~s~~~~~~vR~~A~~~l~~l~~~~~~~l~~~li~~l~~~ 252 (339)
T PF12074_consen 174 ASEEDLCWLLRALEALLSDHPSELSSDK-SSAWAQAFIYLLCSSNVSWKVRRAALSALKKLYASNPELLSKSLISGLWKW 252 (339)
T ss_pred CCHhHHHHHHHHHHHHHhcchhhhhhhH-HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHhChHHHHHHHHHHHHHH
Confidence 4677777788889998888766654444 4566777777664 44688999999999998876644322223355 7888
Q ss_pred hhhCCC
Q psy6184 102 MTDKGF 107 (156)
Q Consensus 102 Lk~~Gi 107 (156)
|.....
T Consensus 253 l~~~~~ 258 (339)
T PF12074_consen 253 LSSSET 258 (339)
T ss_pred HHhccc
Confidence 776553
No 135
>COG5096 Vesicle coat complex, various subunits [Intracellular trafficking and secretion]
Probab=22.44 E-value=4.9e+02 Score=25.29 Aligned_cols=63 Identities=22% Similarity=0.271 Sum_probs=40.8
Q ss_pred CChHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHH----HHHHhhccCCcHHHHHHHHHHHHHH
Q psy6184 8 IVPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFME----QMKELVRGTQHEEVKAKILELIQAW 83 (156)
Q Consensus 8 ~~~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~----~l~kl~~~~~~~~Vk~kil~li~~W 83 (156)
.-+..|+..++|=++|+||...-.||..+-.+ .-.+++. .+++++. .++..||+.+.-.|..-
T Consensus 88 ~~~lLavNti~kDl~d~N~~iR~~AlR~ls~l------------~~~el~~~~~~~ik~~l~-d~~ayVRk~Aalav~kl 154 (757)
T COG5096 88 ELALLAVNTIQKDLQDPNEEIRGFALRTLSLL------------RVKELLGNIIDPIKKLLT-DPHAYVRKTAALAVAKL 154 (757)
T ss_pred HHHHHHHHHHHhhccCCCHHHHHHHHHHHHhc------------ChHHHHHHHHHHHHHHcc-CCcHHHHHHHHHHHHHH
Confidence 44667889999999999999988888655433 2234444 4444444 35667876665544443
No 136
>KOG0196|consensus
Probab=22.37 E-value=1.2e+02 Score=29.90 Aligned_cols=123 Identities=13% Similarity=0.179 Sum_probs=73.3
Q ss_pred HHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhc--c--CCcHHHHHHHHHHHHHHHHHhhCCC
Q psy6184 16 SIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVR--G--TQHEEVKAKILELIQAWAHAFRNSP 91 (156)
Q Consensus 16 aL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~--~--~~~~~Vk~kil~li~~Wa~~F~~~~ 91 (156)
||.-|-...-..|=-+.+.+.|.| -=|++=.=+..+++.++.+..=.. . .-+..+-+ -|+.+|+.+=...|
T Consensus 805 AIa~RKFTsASDVWSyGIVmWEVm--SyGERPYWdmSNQdVIkaIe~gyRLPpPmDCP~aL~q---LMldCWqkdR~~RP 879 (996)
T KOG0196|consen 805 AIAYRKFTSASDVWSYGIVMWEVM--SYGERPYWDMSNQDVIKAIEQGYRLPPPMDCPAALYQ---LMLDCWQKDRNRRP 879 (996)
T ss_pred HhhhcccCchhhccccceEEEEec--ccCCCcccccchHHHHHHHHhccCCCCCCCCcHHHHH---HHHHHHHHHhhcCC
Confidence 444444444455555666666655 345555666777888888776332 1 12233332 35789999977889
Q ss_pred CCcchH-HHHHhhhCCCCCCCC-CCCCCCChhhhhhhhhccccccCCccccccCcchHHHHHhhh
Q psy6184 92 KYRAVP-TKSWMTDKGFKNPSK-SSDSLGLELQIFRICHIHFSEIKGIDQIVDSSSSVALWLRHF 154 (156)
Q Consensus 92 ~l~~i~-~Y~~Lk~~Gi~FP~~-~~~a~f~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~ 154 (156)
.|..|. +.++|.++ |.+ ...+-+.+...++++..+-++... -=||..||++.
T Consensus 880 ~F~qiV~~lDklIrn----P~SLk~~~~~~~r~s~~lld~~~~~~~~-------f~sv~~WL~aI 933 (996)
T KOG0196|consen 880 KFAQIVSTLDKLIRN----PNSLKTIAPESPRPSQPLLDRSGSDFTP-------FRSVGDWLEAI 933 (996)
T ss_pred CHHHHHHHHHHHhcC----chhhcccCCCCCCCcccccCCCCCCCcc-------cCCHHHHHHHh
Confidence 999999 98888774 431 233344444555555544444332 23688898763
No 137
>PF05804 KAP: Kinesin-associated protein (KAP)
Probab=22.17 E-value=2.1e+02 Score=27.39 Aligned_cols=71 Identities=18% Similarity=0.266 Sum_probs=50.8
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHH
Q psy6184 11 SHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWA 84 (156)
Q Consensus 11 k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa 84 (156)
+..+..|.+-|.+.|....+.++++|.-|.-.-.- ..+++....+..|.++++.. +.++.+..+.++...+
T Consensus 289 ~~iV~~Lv~~Ldr~n~ellil~v~fLkkLSi~~EN--K~~m~~~giV~kL~kLl~s~-~~~l~~~aLrlL~NLS 359 (708)
T PF05804_consen 289 KGIVSLLVKCLDRENEELLILAVTFLKKLSIFKEN--KDEMAESGIVEKLLKLLPSE-NEDLVNVALRLLFNLS 359 (708)
T ss_pred cCCHHHHHHHHcCCCHHHHHHHHHHHHHHcCCHHH--HHHHHHcCCHHHHHHHhcCC-CHHHHHHHHHHHHHhC
Confidence 45677888889999999999999999987632221 45566667888888888653 4566666676666655
No 138
>PF01397 Terpene_synth: Terpene synthase, N-terminal domain; InterPro: IPR001906 Sequences containing this domain belong to the terpene synthase family. It has been suggested that this gene family be designated tps (for terpene synthase). Sequence comparisons reveal similarities between the monoterpene (C10) synthases, sesquiterpene (C15) synthases and the diterpene (C20) synthases. It has been split into six subgroups on the basis of phylogeny, called Tpsa-Tpsf []. Tpsa includes vetispiridiene synthase Q39979 from SWISSPROT, 5-epi- aristolochene synthase, Q40577 from SWISSPROT and (+)-delta-cadinene synthase P93665 from SWISSPROT . Tpsb includes (-)-limonene synthase, Q40322 from SWISSPROT. Tpsc includes copalyl diphosphate synthase (kaurene synthase A), O04408 from SWISSPROT. Tpsd includes taxadiene synthase, Q41594 from SWISSPROT, pinene synthase, O24475 from SWISSPROT and myrcene synthase, O24474 from SWISSPROT. Tpse includes ent-kaurene synthase B Q39548 from SWISSPROT. Tpsf includes linalool synthase Q9ZPN5 from SWISSPROT. In the fungus Phaeosphaeria sp. (strain L487) the synthesis of ent-kaurene from geranylgeranyl dophosphate is promoted by a single bifunctional protein [].; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 2ONH_A 2ONG_B 3P5R_A 3P5P_A 3N0F_A 3N0G_B 3PYB_A 3PYA_A 3G4F_A 3G4D_B ....
Probab=22.08 E-value=68 Score=25.29 Aligned_cols=42 Identities=12% Similarity=0.265 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCcchH-HHHHhhhCCCCCCC
Q psy6184 70 EEVKAKILELIQAWAHAFRNSPKYRAVP-TKSWMTDKGFKNPS 111 (156)
Q Consensus 70 ~~Vk~kil~li~~Wa~~F~~~~~l~~i~-~Y~~Lk~~Gi~FP~ 111 (156)
.+|++-+-.+...|...-....++.... .++.||..||.-|+
T Consensus 67 ~EI~~~L~~i~~~~~~~~~~~~dL~~~AL~FRLLRqhGy~VS~ 109 (183)
T PF01397_consen 67 DEIKEILDSIYRSWDEDNEEIDDLYTTALRFRLLRQHGYYVSS 109 (183)
T ss_dssp HHHHHHHHHHHHTTTTTSHTSSCHHHHHHHHHHHHHTT----G
T ss_pred HHHHHHHHHHhhhccccccccCchhHHHHHHHHHHHcCCcccH
Confidence 4444444444445554432223677778 99999999998765
No 139
>COG5369 Uncharacterized conserved protein [Function unknown]
Probab=22.05 E-value=2.1e+02 Score=27.13 Aligned_cols=72 Identities=11% Similarity=0.151 Sum_probs=51.9
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHH
Q psy6184 13 ALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAH 85 (156)
Q Consensus 13 AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~ 85 (156)
.+-.|-+-+.+++...|-.++-+|..+|-||....+.+.-.+-=++.+...+++ +.-.|+..++.+++...-
T Consensus 474 iIdvl~~~v~sKDdaLqans~wvlrHlmyncq~~ekf~~Lakig~~kvl~~~ND-pc~~vq~q~lQilrNftc 545 (743)
T COG5369 474 IIDVLVNLVMSKDDALQANSEWVLRHLMYNCQKNEKFKFLAKIGVEKVLSYTND-PCFKVQHQVLQILRNFTC 545 (743)
T ss_pred HHHHHHHHhhcchhhhhhcchhhhhhhhhcCcchhhhhhHHhcCHHHHHHHhcC-cccccHHHHHHHHHhccc
Confidence 345666777788888888889999999999988865544333334444444443 567899999999998876
No 140
>PF09712 PHA_synth_III_E: Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E)
Probab=21.42 E-value=2.6e+02 Score=23.57 Aligned_cols=89 Identities=10% Similarity=0.190 Sum_probs=60.0
Q ss_pred HHHHHHHHHHhc-CCCHHHHHHHH-HHHHHHHHccchhHHhhhccHHHHHHHHHhhccCCcHHHHHHHHHHHHHHHHHhh
Q psy6184 11 SHALASIKKKLT-NSNPHIVLYAL-LVLESCVKNCGNLIHDEVGTKAFMEQMKELVRGTQHEEVKAKILELIQAWAHAFR 88 (156)
Q Consensus 11 k~AvraL~KrL~-~~n~~v~l~AL-~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~~~~~~~~Vk~kil~li~~Wa~~F~ 88 (156)
.+++..+..+|. ........-+. .+-|.=++.|...|-..++|.+|...+.++++. ...+|...=+++..+-..+.
T Consensus 190 ~~a~~~~~~~l~~~~~~g~~~~s~re~~d~Wi~~ae~~~~~~~~S~ef~~~~g~~~~a--~m~~r~~~~~~~e~~L~~l~ 267 (293)
T PF09712_consen 190 MKAFERMMEKLQERAEEGEQIKSWREFYDIWIDAAEEAYEELFRSEEFAQAYGQLVNA--LMDLRKQQQEVVEEYLRSLN 267 (293)
T ss_pred HHHHHHHHHHHHHhhccCCCCcCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHCC
Confidence 456677777773 21111212122 566888899999999999999999999999974 45678888888888887764
Q ss_pred CCCCCcchH-HHHHh
Q psy6184 89 NSPKYRAVP-TKSWM 102 (156)
Q Consensus 89 ~~~~l~~i~-~Y~~L 102 (156)
-|.=+.|. +|+.|
T Consensus 268 -lPTr~evd~l~k~l 281 (293)
T PF09712_consen 268 -LPTRSEVDELYKRL 281 (293)
T ss_pred -CCCHHHHHHHHHHH
Confidence 23322344 55544
No 141
>smart00523 DWA Domain A in dwarfin family proteins.
Probab=21.26 E-value=1e+02 Score=22.50 Aligned_cols=29 Identities=31% Similarity=0.279 Sum_probs=18.5
Q ss_pred ChHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccc
Q psy6184 9 VPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCG 44 (156)
Q Consensus 9 ~~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG 44 (156)
-++-++.+|.|||+.+ .|..|...|..-|
T Consensus 5 ~~~k~~~sL~KklK~k-------~le~L~~AV~s~g 33 (109)
T smart00523 5 WAKKATESLLKKLKKK-------QLEELLQAVESKG 33 (109)
T ss_pred HHHHHHHHHHHHHHHH-------HHHHHHHHHHcCC
Confidence 3567888999999875 3444444444444
No 142
>PF11426 Tn7_TnsC_Int: Tn7 transposition regulator TnsC; InterPro: IPR021542 TnsC is a molecular switch that regulates transposition and interacts with TnsA which is a component of the transposase. The two proteins interact via the residues 504-555 on TnsC. The TnsA/TnsC interaction is very important in Tn7 transposition []. ; PDB: 1T0F_C.
Probab=21.25 E-value=65 Score=20.14 Aligned_cols=13 Identities=8% Similarity=0.049 Sum_probs=10.6
Q ss_pred HHHHhhhCCCCCC
Q psy6184 98 TKSWMTDKGFKNP 110 (156)
Q Consensus 98 ~Y~~Lk~~Gi~FP 110 (156)
+|+.|+.+|+.|.
T Consensus 27 ~y~~Lk~~Glifd 39 (48)
T PF11426_consen 27 VYEALKQNGLIFD 39 (48)
T ss_dssp HHHHHHHTTSB--
T ss_pred HHHHHHHCCeeee
Confidence 9999999999885
No 143
>PF00514 Arm: Armadillo/beta-catenin-like repeat; InterPro: IPR000225 The armadillo (Arm) repeat is an approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila melanogaster segment polarity gene armadillo involved in signal transduction through wingless. Animal Arm-repeat proteins function in various processes, including intracellular signalling and cytoskeletal regulation, and include such proteins as beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumour suppressor protein, and the nuclear transport factor importin-alpha, amongst others []. A subset of these proteins is conserved across eukaryotic kingdoms. In higher plants, some Arm-repeat proteins function in intracellular signalling like their mammalian counterparts, while others have novel functions []. The 3-dimensional fold of an armadillo repeat is known from the crystal structure of beta-catenin, where the 12 repeats form a superhelix of alpha helices with three helices per unit []. The cylindrical structure features a positively charged grove, which presumably interacts with the acidic surfaces of the known interaction partners of beta-catenin.; GO: 0005515 protein binding; PDB: 2Z6G_A 1IQ1_C 3RZX_A 2C1M_A 3BTR_C 3OQS_A 3TPO_A 1IAL_A 1Q1S_C 1PJM_B ....
Probab=21.18 E-value=1.7e+02 Score=16.43 Aligned_cols=27 Identities=15% Similarity=0.241 Sum_probs=22.2
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHH
Q psy6184 13 ALASIKKKLTNSNPHIVLYALLVLESC 39 (156)
Q Consensus 13 AvraL~KrL~~~n~~v~l~AL~LLe~~ 39 (156)
++..|.+-|.+.++.++..|+..|-.+
T Consensus 13 ~i~~Lv~ll~~~~~~v~~~a~~al~nl 39 (41)
T PF00514_consen 13 GIPPLVQLLKSPDPEVQEEAAWALGNL 39 (41)
T ss_dssp HHHHHHHHTTSSSHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 577788888999999999998877654
No 144
>KOG0213|consensus
Probab=21.11 E-value=1.4e+02 Score=29.39 Aligned_cols=33 Identities=24% Similarity=0.386 Sum_probs=26.2
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHH---HHHccch
Q psy6184 13 ALASIKKKLTNSNPHIVLYALLVLES---CVKNCGN 45 (156)
Q Consensus 13 AvraL~KrL~~~n~~v~l~AL~LLe~---~vkNCG~ 45 (156)
.+-.|.+||+++.|+|-.+|+.|+-. .+|+||+
T Consensus 800 i~stiL~rLnnksa~vRqqaadlis~la~Vlktc~e 835 (1172)
T KOG0213|consen 800 ICSTILWRLNNKSAKVRQQAADLISSLAKVLKTCGE 835 (1172)
T ss_pred HHHHHHHHhcCCChhHHHHHHHHHHHHHHHHHhccH
Confidence 35578899999999999999977654 5678855
No 145
>KOG2171|consensus
Probab=21.01 E-value=5.3e+02 Score=26.17 Aligned_cols=71 Identities=15% Similarity=0.277 Sum_probs=53.1
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhh-c--cCCcHHHHHHHHHHHHHHHHHhhCC
Q psy6184 14 LASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELV-R--GTQHEEVKAKILELIQAWAHAFRNS 90 (156)
Q Consensus 14 vraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~-~--~~~~~~Vk~kil~li~~Wa~~F~~~ 90 (156)
...+-.-|++.++..-.-||..+-..+.=|++.+..+ ++++..++ + +.++..||.-++..|.+.+.+|..+
T Consensus 350 ~~~l~~~l~S~~w~~R~AaL~Als~i~EGc~~~m~~~------l~~Il~~Vl~~l~DphprVr~AA~naigQ~stdl~p~ 423 (1075)
T KOG2171|consen 350 FEALEAMLQSTEWKERHAALLALSVIAEGCSDVMIGN------LPKILPIVLNGLNDPHPRVRYAALNAIGQMSTDLQPE 423 (1075)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHcccHHHHHHH------HHHHHHHHHhhcCCCCHHHHHHHHHHHHhhhhhhcHH
Confidence 3455566678888888888888888889998776654 44444433 2 2578999999999999999999843
No 146
>KOG1820|consensus
Probab=20.76 E-value=6e+02 Score=24.92 Aligned_cols=87 Identities=17% Similarity=0.194 Sum_probs=59.3
Q ss_pred ChHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHccchhHHhhhccHHHHHHHHHhh-c--cCCcHHHHHHHHHHHHHHHH
Q psy6184 9 VPSHALASIKKKLTNSNPHIVLYALLVLESCVKNCGNLIHDEVGTKAFMEQMKELV-R--GTQHEEVKAKILELIQAWAH 85 (156)
Q Consensus 9 ~~k~AvraL~KrL~~~n~~v~l~AL~LLe~~vkNCG~~fh~eIask~Fl~~l~kl~-~--~~~~~~Vk~kil~li~~Wa~ 85 (156)
.--+.+++|.--++++||..-..++.+++-|+++-|.. ...++-...++..+ + +.++.+||.-.++.+-.-..
T Consensus 368 ~l~~~~~~I~e~lk~knp~~k~~~~~~l~r~~~~~~~~----~~~~~t~~~l~p~~~~~~~D~~~~VR~Aa~e~~~~v~k 443 (815)
T KOG1820|consen 368 PLSKMSEAILEALKGKNPQIKGECLLLLDRKLRKLGPK----TVEKETVKTLVPHLIKHINDTDKDVRKAALEAVAAVMK 443 (815)
T ss_pred cHHHHHHHHHHHhcCCChhhHHHHHHHHHHHHhhcCCc----CcchhhHHHHhHHHhhhccCCcHHHHHHHHHHHHHHHH
Confidence 34456677777789999999999999999999999852 33344444544432 2 24688999988888877777
Q ss_pred HhhCCCCCcchH-HH
Q psy6184 86 AFRNSPKYRAVP-TK 99 (156)
Q Consensus 86 ~F~~~~~l~~i~-~Y 99 (156)
-|....--.++. +|
T Consensus 444 ~~Ge~~~~k~L~~~~ 458 (815)
T KOG1820|consen 444 VHGEEVFKKLLKDLD 458 (815)
T ss_pred HhhHHHHHHHHHhhc
Confidence 665433223334 44
No 147
>PLN00047 photosystem II biogenesis protein Psb29; Provisional
Probab=20.09 E-value=22 Score=30.27 Aligned_cols=63 Identities=10% Similarity=0.295 Sum_probs=36.4
Q ss_pred HHHHHHHHHhhccCCcHHHHHHHHHH-HHHHHHHhhCCCCCcc-hH-HHHHhhhCCCCCCCCCCCCCC
Q psy6184 54 KAFMEQMKELVRGTQHEEVKAKILEL-IQAWAHAFRNSPKYRA-VP-TKSWMTDKGFKNPSKSSDSLG 118 (156)
Q Consensus 54 k~Fl~~l~kl~~~~~~~~Vk~kil~l-i~~Wa~~F~~~~~l~~-i~-~Y~~Lk~~Gi~FP~~~~~a~f 118 (156)
+.|.+..-..|..-...-|.+.+.++ +..-...|..||=|.. +. +|+.+-. ||+ |+.+.+++|
T Consensus 63 r~F~~~yp~pIpsiYrrvvdELLVElHLLs~n~~F~yDplFALGlVtvfd~fm~-GY~-Pee~~~~IF 128 (283)
T PLN00047 63 AKFLKSYKRPIPSIYSTVLQELLVQQHLMRYKKTYRYDPVFALGFVTVYDQLME-GYP-SDEDRDAIF 128 (283)
T ss_pred HHHHHhCCCCCcHHHHHHHHHHHHHHHHHHhccCceeCchhhhhhHHHHHHHHc-cCC-ChHHHHHHH
Confidence 45555555544432223344444444 3344457887877654 66 9999875 886 666666654
Done!