Query psy10447
Match_columns 166
No_of_seqs 95 out of 113
Neff 3.6
Searched_HMMs 46136
Date Fri Aug 16 18:23:37 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10447.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10447hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0213|consensus 100.0 5.4E-74 1.2E-78 544.3 15.4 161 5-165 583-743 (1172)
2 COG5181 HSH155 U2 snRNP splice 100.0 2.6E-60 5.7E-65 445.8 11.6 161 5-165 388-548 (975)
3 PF01602 Adaptin_N: Adaptin N 96.2 0.15 3.3E-06 44.8 13.1 137 15-165 230-367 (526)
4 PTZ00429 beta-adaptin; Provisi 95.0 0.46 9.9E-06 46.7 12.7 124 32-165 272-395 (746)
5 PF12348 CLASP_N: CLASP N term 95.0 0.38 8.2E-06 38.3 10.2 140 16-164 53-203 (228)
6 cd00020 ARM Armadillo/beta-cat 94.6 0.28 6.1E-06 33.7 7.4 72 18-90 9-81 (120)
7 PF13646 HEAT_2: HEAT repeats; 94.4 0.3 6.5E-06 32.9 7.1 85 61-163 2-88 (88)
8 PF12460 MMS19_C: RNAPII trans 94.0 0.41 9E-06 42.7 9.0 78 12-89 319-396 (415)
9 PF13646 HEAT_2: HEAT repeats; 91.2 0.57 1.2E-05 31.5 4.8 45 121-165 14-58 (88)
10 PF12719 Cnd3: Nuclear condens 90.6 1.1 2.4E-05 38.1 7.0 93 37-164 48-140 (298)
11 PF10508 Proteasom_PSMB: Prote 90.3 4.5 9.8E-05 37.4 11.2 146 14-165 75-229 (503)
12 COG4748 Uncharacterized conser 88.2 0.74 1.6E-05 42.1 4.4 60 53-114 171-230 (365)
13 PF02985 HEAT: HEAT repeat; I 88.0 0.5 1.1E-05 27.7 2.2 27 139-165 1-27 (31)
14 PF10274 ParcG: Parkin co-regu 86.3 2.8 6.1E-05 35.0 6.5 119 14-143 36-174 (183)
15 PTZ00429 beta-adaptin; Provisi 86.1 4.2 9.2E-05 40.2 8.7 96 58-165 33-132 (746)
16 PF05004 IFRD: Interferon-rela 83.5 4.7 0.0001 35.3 7.0 68 16-83 174-253 (309)
17 KOG3961|consensus 82.7 1.8 3.9E-05 38.1 4.1 77 58-137 155-243 (262)
18 PF01602 Adaptin_N: Adaptin N 82.0 25 0.00053 31.1 10.9 117 37-165 173-294 (526)
19 PF06575 DUF1132: Protein of u 81.8 0.76 1.6E-05 35.2 1.2 18 99-116 35-52 (95)
20 KOG1060|consensus 80.6 4.4 9.6E-05 41.2 6.3 68 95-164 350-418 (968)
21 PRK09687 putative lyase; Provi 80.4 9.2 0.0002 32.9 7.6 32 133-164 154-185 (280)
22 PF01603 B56: Protein phosphat 80.4 5.2 0.00011 36.2 6.3 88 11-105 93-180 (409)
23 PF00134 Cyclin_N: Cyclin, N-t 79.0 16 0.00035 26.1 7.4 92 71-165 27-122 (127)
24 PF01347 Vitellogenin_N: Lipop 78.4 24 0.00052 32.5 10.0 91 71-165 448-551 (618)
25 KOG1243|consensus 77.7 5.4 0.00012 39.5 5.9 77 55-137 327-403 (690)
26 PF13513 HEAT_EZ: HEAT-like re 74.6 19 0.0004 22.7 6.4 48 35-83 6-53 (55)
27 PRK09687 putative lyase; Provi 74.0 29 0.00064 29.8 8.9 90 56-165 190-280 (280)
28 PF12755 Vac14_Fab1_bd: Vacuol 72.0 35 0.00076 25.2 7.8 72 32-118 9-81 (97)
29 PF10381 Autophagy_Cterm: Auto 65.0 5.3 0.00012 24.0 1.7 19 33-51 5-23 (25)
30 TIGR00207 fliG flagellar motor 63.6 48 0.001 29.5 8.3 76 19-108 109-191 (338)
31 cd00020 ARM Armadillo/beta-cat 63.1 31 0.00067 23.4 5.6 69 17-86 50-119 (120)
32 PF13513 HEAT_EZ: HEAT-like re 62.5 11 0.00023 23.9 3.0 31 135-165 25-55 (55)
33 PF04914 DltD_C: DltD C-termin 62.1 7.5 0.00016 30.6 2.6 73 68-154 31-103 (130)
34 cd07920 Pumilio Pumilio-family 61.5 37 0.00081 28.3 6.8 21 125-145 190-210 (322)
35 KOG3666|consensus 60.4 30 0.00064 35.5 6.9 53 31-83 566-628 (1141)
36 PF12348 CLASP_N: CLASP N term 59.6 86 0.0019 24.8 9.2 102 58-164 53-157 (228)
37 COG5096 Vesicle coat complex, 59.1 34 0.00074 34.4 7.1 50 38-90 38-87 (757)
38 KOG4464|consensus 58.6 5.1 0.00011 38.3 1.3 83 22-104 234-361 (532)
39 PF02985 HEAT: HEAT repeat; I 58.4 20 0.00044 20.7 3.5 28 59-86 1-28 (31)
40 PF14664 RICTOR_N: Rapamycin-i 58.4 50 0.0011 29.9 7.5 97 63-164 30-134 (371)
41 PF08784 RPA_C: Replication pr 58.3 9.5 0.00021 27.5 2.4 31 70-100 44-75 (102)
42 PF10508 Proteasom_PSMB: Prote 56.8 1.5E+02 0.0033 27.5 10.5 124 35-164 57-186 (503)
43 PRK13800 putative oxidoreducta 56.5 53 0.0011 32.7 7.9 87 61-165 778-865 (897)
44 smart00185 ARM Armadillo/beta- 55.7 28 0.0006 20.0 3.8 28 59-86 13-40 (41)
45 PF14631 FancD2: Fanconi anaem 54.0 1.8E+02 0.0038 31.4 11.5 142 15-164 345-499 (1426)
46 KOG1232|consensus 53.6 15 0.00033 35.0 3.5 132 5-151 270-433 (511)
47 PF00514 Arm: Armadillo/beta-c 52.7 33 0.00072 20.6 3.9 29 58-86 12-40 (41)
48 TIGR00569 ccl1 cyclin ccl1. Un 52.1 49 0.0011 29.4 6.3 47 103-150 84-131 (305)
49 PF03224 V-ATPase_H_N: V-ATPas 51.3 79 0.0017 27.0 7.3 138 20-164 15-176 (312)
50 PF05002 SGS: SGS domain ; In 50.1 13 0.00027 27.6 2.0 29 59-87 26-54 (82)
51 PF12755 Vac14_Fab1_bd: Vacuol 49.6 45 0.00097 24.7 4.9 67 11-78 22-88 (97)
52 COG2947 Uncharacterized conser 49.6 5.9 0.00013 32.8 0.2 30 8-40 13-42 (156)
53 KOG0212|consensus 49.3 52 0.0011 32.7 6.4 129 24-163 223-361 (675)
54 TIGR01716 RGG_Cterm transcript 46.9 31 0.00067 27.3 3.9 49 36-86 87-135 (220)
55 smart00708 PhBP Insect pheromo 46.7 69 0.0015 21.8 5.2 70 31-108 30-99 (103)
56 cd01042 DMQH Demethoxyubiquino 46.3 37 0.00081 27.8 4.3 43 16-69 61-103 (165)
57 smart00638 LPD_N Lipoprotein N 46.2 1.9E+02 0.0042 26.6 9.4 49 116-165 456-507 (574)
58 PF09337 zf-H2C2: His(2)-Cys(2 45.7 15 0.00033 23.4 1.6 24 63-88 15-38 (39)
59 smart00229 RasGEFN Guanine nuc 45.5 58 0.0012 23.8 4.9 53 56-110 42-105 (127)
60 PF14500 MMS19_N: Dos2-interac 44.8 77 0.0017 27.3 6.2 51 53-110 203-253 (262)
61 PLN03200 cellulose synthase-in 42.8 2E+02 0.0044 32.4 10.2 148 18-165 566-721 (2102)
62 cd01392 HTH_LacI Helix-turn-he 41.9 57 0.0012 20.1 3.9 37 129-165 2-39 (52)
63 PF14561 TPR_20: Tetratricopep 41.9 33 0.00071 24.9 3.1 43 57-100 43-85 (90)
64 cd06561 AlkD_like A new struct 41.5 55 0.0012 25.3 4.5 44 107-159 118-161 (197)
65 PF04818 CTD_bind: RNA polymer 41.4 33 0.00072 22.8 2.8 22 62-83 34-55 (64)
66 PF00140 Sigma70_r1_2: Sigma-7 40.7 35 0.00077 21.1 2.7 27 32-59 3-29 (37)
67 PF06371 Drf_GBD: Diaphanous G 40.7 62 0.0013 24.8 4.6 52 32-86 132-186 (187)
68 PF12717 Cnd1: non-SMC mitotic 38.6 1.9E+02 0.0042 22.7 7.9 85 59-148 26-139 (178)
69 cd00043 CYCLIN Cyclin box fold 37.9 1.1E+02 0.0023 19.5 5.7 81 76-159 3-85 (88)
70 cd03571 ENTH_epsin ENTH domain 37.5 19 0.00042 27.9 1.4 46 1-47 22-67 (123)
71 PF04542 Sigma70_r2: Sigma-70 37.4 57 0.0012 20.7 3.4 30 12-41 25-57 (71)
72 cd07920 Pumilio Pumilio-family 36.7 1.8E+02 0.0039 24.2 7.1 33 128-163 271-303 (322)
73 PRK06922 hypothetical protein; 36.0 79 0.0017 31.5 5.5 72 44-117 290-392 (677)
74 PF12765 Cohesin_HEAT: HEAT re 35.9 42 0.00092 21.3 2.5 28 135-162 15-42 (42)
75 PF00356 LacI: Bacterial regul 35.7 59 0.0013 21.2 3.2 40 127-166 2-42 (46)
76 PF08064 UME: UME (NUC010) dom 35.5 75 0.0016 23.6 4.2 47 35-84 34-80 (107)
77 PF08623 TIP120: TATA-binding 35.4 52 0.0011 27.1 3.6 33 72-111 132-165 (169)
78 PF13877 RPAP3_C: Potential Mo 35.0 69 0.0015 22.7 3.8 67 19-89 11-79 (94)
79 PF08389 Xpo1: Exportin 1-like 35.0 1.1E+02 0.0023 22.1 4.9 57 13-71 79-139 (148)
80 KOG0211|consensus 34.7 3.3E+02 0.0071 27.6 9.5 83 70-163 530-621 (759)
81 PF11113 Phage_head_chap: Head 34.3 24 0.00052 24.8 1.3 25 63-87 29-53 (56)
82 KOG3260|consensus 34.2 36 0.00079 29.5 2.6 27 56-82 183-209 (224)
83 PF08158 NUC130_3NT: NUC130/3N 32.7 1.2E+02 0.0026 20.5 4.5 35 49-83 10-44 (52)
84 KOG2171|consensus 32.4 3.1E+02 0.0066 29.1 9.1 103 55-164 33-144 (1075)
85 PF02854 MIF4G: MIF4G domain; 31.8 1.3E+02 0.0028 22.6 5.0 62 98-163 17-80 (209)
86 PF05402 PqqD: Coenzyme PQQ sy 31.5 93 0.002 20.4 3.8 32 56-87 32-63 (68)
87 PF08389 Xpo1: Exportin 1-like 31.0 1.1E+02 0.0024 22.0 4.4 43 63-107 91-134 (148)
88 cd07064 AlkD_like_1 A new stru 31.0 3E+02 0.0065 22.6 10.6 43 107-159 128-170 (208)
89 PF06743 FAST_1: FAST kinase-l 30.9 1.8E+02 0.0039 20.0 6.0 68 34-106 2-69 (71)
90 PHA00148 lower collar protein 30.7 36 0.00078 30.0 2.0 25 92-117 44-68 (242)
91 PF01417 ENTH: ENTH domain; I 30.5 28 0.00061 26.0 1.2 47 1-47 24-70 (125)
92 PF13212 DUF4020: Domain of un 30.5 1.9E+02 0.0042 24.5 6.2 57 28-85 56-125 (180)
93 TIGR03495 phage_LysB phage lys 30.4 20 0.00044 28.7 0.5 19 140-158 80-98 (135)
94 cd05498 Bromo_Brdt_II_like Bro 30.3 1.4E+02 0.0031 21.5 4.9 82 21-109 8-102 (102)
95 COG1413 FOG: HEAT repeat [Ener 30.1 92 0.002 26.2 4.4 32 134-165 70-101 (335)
96 KOG1020|consensus 29.5 7.5E+02 0.016 27.7 11.5 140 12-165 812-958 (1692)
97 TIGR01446 DnaD_dom DnaD and ph 29.4 1.7E+02 0.0036 19.6 4.8 46 56-106 17-62 (73)
98 KOG2137|consensus 29.3 1.9E+02 0.0042 29.1 6.9 26 69-94 381-406 (700)
99 PF05536 Neurochondrin: Neuroc 28.7 1.7E+02 0.0037 27.8 6.3 86 4-90 126-216 (543)
100 KOG0166|consensus 28.6 4.3E+02 0.0093 25.7 8.9 142 18-164 281-483 (514)
101 PRK09623 vorD 2-ketoisovalerat 28.6 12 0.00027 27.6 -1.0 23 67-89 5-27 (105)
102 PF07571 DUF1546: Protein of u 28.5 1.6E+02 0.0035 21.4 4.9 36 52-87 22-57 (92)
103 PF10266 Strumpellin: Heredita 27.9 4.5E+02 0.0098 27.9 9.5 80 4-83 526-618 (1081)
104 PLN03200 cellulose synthase-in 27.8 6.6E+02 0.014 28.7 11.1 143 17-164 447-590 (2102)
105 PF04826 Arm_2: Armadillo-like 27.4 1.5E+02 0.0034 25.4 5.3 69 35-106 114-182 (254)
106 COG1413 FOG: HEAT repeat [Ener 27.2 3.1E+02 0.0068 23.0 7.1 91 57-165 42-133 (335)
107 PF12824 MRP-L20: Mitochondria 27.2 95 0.0021 25.4 3.8 40 123-162 103-142 (164)
108 PF05327 RRN3: RNA polymerase 27.1 1.5E+02 0.0033 28.1 5.7 71 31-109 51-121 (563)
109 PF11701 UNC45-central: Myosin 27.1 1.2E+02 0.0025 23.9 4.2 60 31-90 58-120 (157)
110 KOG2137|consensus 26.8 3E+02 0.0065 27.8 7.7 121 18-148 354-474 (700)
111 cd03572 ENTH_epsin_related ENT 26.7 75 0.0016 24.9 3.0 33 57-89 37-69 (122)
112 PF15565 Imm16: Immunity prote 26.7 70 0.0015 24.7 2.8 37 29-73 62-99 (106)
113 PF08445 FR47: FR47-like prote 25.5 39 0.00084 23.8 1.2 13 26-38 31-43 (86)
114 PF08780 NTase_sub_bind: Nucle 25.2 1.2E+02 0.0025 23.3 3.8 30 11-49 33-62 (124)
115 PF10948 DUF2635: Protein of u 25.1 37 0.00081 22.7 0.9 11 105-115 27-37 (47)
116 PF03568 Peptidase_C50: Peptid 24.7 59 0.0013 29.2 2.4 19 106-124 68-86 (383)
117 KOG1824|consensus 24.5 5.9E+02 0.013 27.4 9.5 98 56-165 855-959 (1233)
118 COG4086 Predicted secreted pro 24.0 1.6E+02 0.0036 26.7 5.0 81 84-166 123-227 (299)
119 PF11919 DUF3437: Domain of un 23.6 91 0.002 23.1 2.8 37 25-69 4-41 (90)
120 KOG4215|consensus 23.4 4E+02 0.0086 25.5 7.5 86 34-151 258-353 (432)
121 PF11423 Repressor_Mnt: Regula 23.0 70 0.0015 20.0 1.8 16 150-165 11-26 (30)
122 PF07725 LRR_3: Leucine Rich R 22.8 19 0.00041 20.4 -0.7 11 16-26 10-20 (20)
123 PF05099 TerB: Tellurite resis 22.5 3.2E+02 0.0068 20.0 7.4 81 75-164 23-105 (140)
124 PF06902 Fer4_19: Divergent 4F 22.5 46 0.001 23.1 1.0 20 69-88 38-57 (64)
125 PRK14350 ligA NAD-dependent DN 22.3 2.1E+02 0.0047 28.2 5.8 82 9-107 478-563 (669)
126 TIGR02412 pepN_strep_liv amino 21.5 4.9E+02 0.011 26.0 8.1 69 97-165 749-822 (831)
127 PF09324 DUF1981: Domain of un 21.4 3.1E+02 0.0068 19.6 5.9 66 97-165 15-86 (86)
128 PF14198 TnpV: Transposon-enco 21.4 2E+02 0.0043 22.0 4.4 57 62-124 50-106 (111)
129 PF11698 V-ATPase_H_C: V-ATPas 21.0 1.8E+02 0.0038 22.9 4.1 33 130-165 81-113 (119)
130 smart00354 HTH_LACI helix_turn 20.7 1.7E+02 0.0038 19.7 3.6 38 128-165 4-42 (70)
131 PRK00865 glutamate racemase; P 20.6 84 0.0018 26.5 2.4 29 2-30 37-65 (261)
132 PF04104 DNA_primase_lrg: Euka 20.6 36 0.00078 29.0 0.2 72 12-95 106-183 (260)
133 COG1317 FliH Flagellar biosynt 20.5 3E+02 0.0064 23.4 5.7 76 82-165 75-153 (234)
134 cd06867 PX_SNX41_42 The phosph 20.5 1.1E+02 0.0024 22.5 2.8 21 26-47 79-99 (112)
135 PF09209 DUF1956: Domain of un 20.4 2.3E+02 0.005 20.1 4.4 44 33-82 5-48 (125)
136 PF00583 Acetyltransf_1: Acety 20.4 61 0.0013 20.8 1.2 13 26-38 35-47 (83)
137 PF12872 OST-HTH: OST-HTH/LOTU 20.1 1.3E+02 0.0028 19.9 2.8 35 70-104 2-37 (74)
No 1
>KOG0213|consensus
Probab=100.00 E-value=5.4e-74 Score=544.34 Aligned_cols=161 Identities=77% Similarity=1.201 Sum_probs=159.8
Q ss_pred ccCCcchhhhhhhhHHHHHHHHhhhcchHHHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHh
Q psy10447 5 HCHTLSIESFDSVLKPLWKGIRTHRGKGLAAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQ 84 (166)
Q Consensus 5 as~PYGIEsFd~VL~plW~Gir~hRGK~LAaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~q 84 (166)
|++|||||+||+||+|||+|||+||||+|||||||||||||||||+||+|||+|||.|++|||+||||||||||||||+|
T Consensus 583 aa~Pygie~fDsVlkpLwkgir~hrgk~laafLkAigyliplmd~eya~yyTrevmlil~rEf~sPDeemkkivLKVv~q 662 (1172)
T KOG0213|consen 583 AATPYGIEQFDSVLKPLWKGIRQHRGKELAAFLKAIGYLIPLMDAEYASYYTREVMLILIREFGSPDEEMKKIVLKVVKQ 662 (1172)
T ss_pred hcCCcchHHHHHHHHHHHHHHHHccChHHHHHHHHHhhccccccHHHHHHhHHHHHHHHHHhhCCChHHHHHHHHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcccCcchhhHhhhhchHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHhhCHHHHHHHhhcccccchHHHHHHHHHHHhh
Q psy10447 85 CCATDGVEAQYIKDEILPPFFKNFWNHRMALDRRNYRQLVDTTVEIANKVGASEIINRVVDDLKDENEQYRKMVMESIEK 164 (166)
Q Consensus 85 c~~t~gv~~~yir~~i~~~FF~~FW~rR~AlDr~~~~~vv~TTv~lA~Kvg~~~il~~iv~~lKDesE~~R~M~~eti~k 164 (166)
||.++||+|+|+|.+|+|+||++||+||||+||+||+|||+|||+||+|+|+.++++|+|.+||||+||||+|++||++|
T Consensus 663 cc~t~Gv~~~y~r~dilp~ff~~fw~rrmA~drr~ykqlv~ttv~ia~KvG~~~~v~R~v~~lkde~e~yrkm~~etv~r 742 (1172)
T KOG0213|consen 663 CCATDGVEPAYIRFDILPEFFFSFWGRRMALDRRNYKQLVDTTVEIAAKVGSDPIVSRVVLDLKDEPEQYRKMVAETVSR 742 (1172)
T ss_pred HhcccCCCHHHHhhhhhHHHHhhhhhhhhhccccchhhHHHHHHHHHHHhCchHHHHHHhhhhccccHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred c
Q psy10447 165 T 165 (166)
Q Consensus 165 v 165 (166)
+
T Consensus 743 i 743 (1172)
T KOG0213|consen 743 I 743 (1172)
T ss_pred H
Confidence 6
No 2
>COG5181 HSH155 U2 snRNP spliceosome subunit [RNA processing and modification]
Probab=100.00 E-value=2.6e-60 Score=445.81 Aligned_cols=161 Identities=44% Similarity=0.717 Sum_probs=159.3
Q ss_pred ccCCcchhhhhhhhHHHHHHHHhhhcchHHHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHh
Q psy10447 5 HCHTLSIESFDSVLKPLWKGIRTHRGKGLAAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQ 84 (166)
Q Consensus 5 as~PYGIEsFd~VL~plW~Gir~hRGK~LAaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~q 84 (166)
+++|||||.||.||+|||+|+++||||.|+|||||+|+||||||||||+|||+|.|+|+-|||+||||||||++|+|+++
T Consensus 388 ~~~Pygie~fd~vl~pLw~g~~~hrgk~l~sfLkA~g~iiplm~peYa~h~tre~m~iv~ref~spdeemkk~~l~v~~~ 467 (975)
T COG5181 388 LVGPYGIEQFDEVLCPLWEGASQHRGKELVSFLKAMGFIIPLMSPEYACHDTREHMEIVFREFKSPDEEMKKDLLVVERI 467 (975)
T ss_pred hcCCcchHHHHHHHHHHHHHHHhcCCchHHHHHHHhccccccCChHhhhhhHHHHHHHHHHHhCCchhhcchhHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcccCcchhhHhhhhchHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHhhCHHHHHHHhhcccccchHHHHHHHHHHHhh
Q psy10447 85 CCATDGVEAQYIKDEILPPFFKNFWNHRMALDRRNYRQLVDTTVEIANKVGASEIINRVVDDLKDENEQYRKMVMESIEK 164 (166)
Q Consensus 85 c~~t~gv~~~yir~~i~~~FF~~FW~rR~AlDr~~~~~vv~TTv~lA~Kvg~~~il~~iv~~lKDesE~~R~M~~eti~k 164 (166)
|..++++||.|+|++|.|+||..||.||+|+||+.|+|||+|||-||++.|+..++++|+++++||+||||+|+.+++.+
T Consensus 468 C~~v~~~tp~~lr~~v~pefF~~fw~rr~A~dr~~~k~v~~ttvilAk~~g~~~v~~kil~~~~De~ep~r~m~a~~vsr 547 (975)
T COG5181 468 CDKVGTDTPWKLRDQVSPEFFSPFWRRRSAGDRRSYKQVVLTTVILAKMGGDPRVSRKILEYYSDEPEPYRKMNAGLVSR 547 (975)
T ss_pred HhccCCCCHHHHHHhhcHHhhchHHHhhhcccccccceeehhHHHHHHHcCChHHHHHHHhhccCCcchhhhhhhHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred c
Q psy10447 165 T 165 (166)
Q Consensus 165 v 165 (166)
+
T Consensus 548 i 548 (975)
T COG5181 548 I 548 (975)
T ss_pred H
Confidence 5
No 3
>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=96.22 E-value=0.15 Score=44.84 Aligned_cols=137 Identities=17% Similarity=0.280 Sum_probs=94.8
Q ss_pred hhhhHHHHHHHHhhhcchHHHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchh
Q psy10447 15 DSVLKPLWKGIRTHRGKGLAAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQ 94 (166)
Q Consensus 15 d~VL~plW~Gir~hRGK~LAaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~ 94 (166)
+.+++++-.-++. ..-|-.+-|+..++=+-+ +.. .-+.++..|.+=.+|+|.+.|-++|.-+.+.+... +.
T Consensus 230 ~~~i~~l~~~l~s---~~~~V~~e~~~~i~~l~~-~~~--~~~~~~~~L~~lL~s~~~nvr~~~L~~L~~l~~~~---~~ 300 (526)
T PF01602_consen 230 NRIIEPLLNLLQS---SSPSVVYEAIRLIIKLSP-SPE--LLQKAINPLIKLLSSSDPNVRYIALDSLSQLAQSN---PP 300 (526)
T ss_dssp HHHHHHHHHHHHH---HHHHHHHHHHHHHHHHSS-SHH--HHHHHHHHHHHHHTSSSHHHHHHHHHHHHHHCCHC---HH
T ss_pred HHHHHHHHHHhhc---cccHHHHHHHHHHHHhhc-chH--HHHhhHHHHHHHhhcccchhehhHHHHHHHhhccc---ch
Confidence 3455555555552 344445666666663332 222 66778888999999999999999999999998887 44
Q ss_pred hHhhhhchHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHhhCHHHHHHHhhcccccc-hHHHHHHHHHHHhhc
Q psy10447 95 YIKDEILPPFFKNFWNHRMALDRRNYRQLVDTTVEIANKVGASEIINRVVDDLKDE-NEQYRKMVMESIEKT 165 (166)
Q Consensus 95 yir~~i~~~FF~~FW~rR~AlDr~~~~~vv~TTv~lA~Kvg~~~il~~iv~~lKDe-sE~~R~M~~eti~kv 165 (166)
++. .+.+..|=. +..-|....+..++.-..++++-++.+|++.+..++++. ++.||+.++.+|.++
T Consensus 301 ~v~----~~~~~~~~l-~~~~d~~Ir~~~l~lL~~l~~~~n~~~Il~eL~~~l~~~~d~~~~~~~i~~I~~l 367 (526)
T PF01602_consen 301 AVF----NQSLILFFL-LYDDDPSIRKKALDLLYKLANESNVKEILDELLKYLSELSDPDFRRELIKAIGDL 367 (526)
T ss_dssp HHG----THHHHHHHH-HCSSSHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHC--HHHHHHHHHHHHHH
T ss_pred hhh----hhhhhhhee-cCCCChhHHHHHHHHHhhcccccchhhHHHHHHHHHHhccchhhhhhHHHHHHHH
Confidence 443 334444422 233455556666788899999999999999999999877 555999999998753
No 4
>PTZ00429 beta-adaptin; Provisional
Probab=95.05 E-value=0.46 Score=46.73 Aligned_cols=124 Identities=15% Similarity=0.124 Sum_probs=87.5
Q ss_pred hHHHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhHhhhhchHHHHHHHHH
Q psy10447 32 GLAAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFKNFWNH 111 (166)
Q Consensus 32 ~LAaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~FW~r 111 (166)
++=+-.|++-.+.|-++++.-.-+.+.+-.-|+. ..|.+.|.|-++|+-+....... |+ ++.++++.|-.+
T Consensus 272 VVl~Aik~il~l~~~~~~~~~~~~~~rl~~pLv~-L~ss~~eiqyvaLr~I~~i~~~~---P~-----lf~~~~~~Ff~~ 342 (746)
T PTZ00429 272 VVMGAIKVVANLASRCSQELIERCTVRVNTALLT-LSRRDAETQYIVCKNIHALLVIF---PN-----LLRTNLDSFYVR 342 (746)
T ss_pred HHHHHHHHHHHhcCcCCHHHHHHHHHHHHHHHHH-hhCCCccHHHHHHHHHHHHHHHC---HH-----HHHHHHHhhhcc
Confidence 3334456666666666665444444444443443 36788999999999998777644 43 444567777666
Q ss_pred HhhhhhhhhhHHHHHHHHHHHhhCHHHHHHHhhcccccchHHHHHHHHHHHhhc
Q psy10447 112 RMALDRRNYRQLVDTTVEIANKVGASEIINRVVDDLKDENEQYRKMVMESIEKT 165 (166)
Q Consensus 112 R~AlDr~~~~~vv~TTv~lA~Kvg~~~il~~iv~~lKDesE~~R~M~~eti~kv 165 (166)
-.--+. ..+.-.+.-+.||+.-++.+|+..|..+..|-+..||+.++.||.++
T Consensus 343 ~~Dp~y-IK~~KLeIL~~Lane~Nv~~IL~EL~eYa~d~D~ef~r~aIrAIg~l 395 (746)
T PTZ00429 343 YSDPPF-VKLEKLRLLLKLVTPSVAPEILKELAEYASGVDMVFVVEVVRAIASL 395 (746)
T ss_pred cCCcHH-HHHHHHHHHHHHcCcccHHHHHHHHHHHhhcCCHHHHHHHHHHHHHH
Confidence 553333 33444488899999999999999999999999999999999999764
No 5
>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=95.02 E-value=0.38 Score=38.26 Aligned_cols=140 Identities=13% Similarity=0.196 Sum_probs=92.1
Q ss_pred hhhHHHHHHHHhhhcchHHHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchhh
Q psy10447 16 SVLKPLWKGIRTHRGKGLAAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQY 95 (166)
Q Consensus 16 ~VL~plW~Gir~hRGK~LAaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~y 95 (166)
.++.++=+.+..-|++....=+.+++.+..-+..+...| ...+++.|.+-..++..-.+......+..++..-+..+
T Consensus 53 ~~~~~i~~~l~d~Rs~v~~~A~~~l~~l~~~l~~~~~~~-~~~~l~~Ll~~~~~~~~~i~~~a~~~L~~i~~~~~~~~-- 129 (228)
T PF12348_consen 53 QLLDAIIKQLSDLRSKVSKTACQLLSDLARQLGSHFEPY-ADILLPPLLKKLGDSKKFIREAANNALDAIIESCSYSP-- 129 (228)
T ss_dssp ---HHHHH-S-HH---HHHHHHHHHHHHHHHHGGGGHHH-HHHHHHHHHHGGG---HHHHHHHHHHHHHHHTTS-H----
T ss_pred HhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhHhHHHH-HHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHCCcHH--
Confidence 344588889999999999999999999998887776666 88999999999999999999999998888887655333
Q ss_pred HhhhhchHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHhhC-----------HHHHHHHhhcccccchHHHHHHHHHHHhh
Q psy10447 96 IKDEILPPFFKNFWNHRMALDRRNYRQLVDTTVEIANKVG-----------ASEIINRVVDDLKDENEQYRKMVMESIEK 164 (166)
Q Consensus 96 ir~~i~~~FF~~FW~rR~AlDr~~~~~vv~TTv~lA~Kvg-----------~~~il~~iv~~lKDesE~~R~M~~eti~k 164 (166)
.++.++...-++.+.+.=|...-..+.. +.++.| ...++.-|...+.|.+..-|..+-+++..
T Consensus 130 ---~~~~~~l~~~~~~Kn~~vR~~~~~~l~~---~l~~~~~~~~~l~~~~~~~~l~~~l~~~l~D~~~~VR~~Ar~~~~~ 203 (228)
T PF12348_consen 130 ---KILLEILSQGLKSKNPQVREECAEWLAI---ILEKWGSDSSVLQKSAFLKQLVKALVKLLSDADPEVREAARECLWA 203 (228)
T ss_dssp ---HHHHHHHHHHTT-S-HHHHHHHHHHHHH---HHTT-----GGG--HHHHHHHHHHHHHHHTSS-HHHHHHHHHHHHH
T ss_pred ---HHHHHHHHHHHhCCCHHHHHHHHHHHHH---HHHHccchHhhhcccchHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Confidence 4445666666666655544433333332 333333 35688899999999999999999887653
No 6
>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=94.58 E-value=0.28 Score=33.73 Aligned_cols=72 Identities=17% Similarity=0.098 Sum_probs=48.9
Q ss_pred hHHHHHHHHhhhcchHHHHHHHHhhhcccCChhHHhhhHH-HHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccC
Q psy10447 18 LKPLWKGIRTHRGKGLAAFLKAIGYLIPLMDAEYANYYTK-EVMLILIREFQSPDEEMKKIVLKVVKQCCATDG 90 (166)
Q Consensus 18 L~plW~Gir~hRGK~LAaFLKaiG~IIPLMD~eyA~yYt~-evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~g 90 (166)
+.+|=+-++...-...-.-+.|++.+.-- +|++.....+ ++++.|..-++++|.+.++..+..+.+.+....
T Consensus 9 i~~l~~~l~~~~~~~~~~a~~~l~~l~~~-~~~~~~~~~~~~~i~~l~~~l~~~~~~v~~~a~~~L~~l~~~~~ 81 (120)
T cd00020 9 LPALVSLLSSSDENVQREAAWALSNLSAG-NNDNIQAVVEAGGLPALVQLLKSEDEEVVKAALWALRNLAAGPE 81 (120)
T ss_pred hHHHHHHHHcCCHHHHHHHHHHHHHHhcC-CHHHHHHHHHCCChHHHHHHHhCCCHHHHHHHHHHHHHHccCcH
Confidence 33343444443335555667777776544 3555444444 999999999999999999999999998876543
No 7
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=94.43 E-value=0.3 Score=32.87 Aligned_cols=85 Identities=15% Similarity=0.351 Sum_probs=57.4
Q ss_pred HHHHhhc-CCCcHHHHHHHHHHHHhhhcccCcchhhHhhhhchHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHhhCHHHH
Q psy10447 61 LILIREF-QSPDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFKNFWNHRMALDRRNYRQLVDTTVEIANKVGASEI 139 (166)
Q Consensus 61 ~il~rEF-~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~FW~rR~AlDr~~~~~vv~TTv~lA~Kvg~~~i 139 (166)
+.|.+.+ ++||...|..+.+++.+.. ..+.+|.+.+.+ .|. + -.|-.+.+.--.++|..+.
T Consensus 2 ~~L~~~l~~~~~~~vr~~a~~~L~~~~----------~~~~~~~L~~~l------~d~-~-~~vr~~a~~aL~~i~~~~~ 63 (88)
T PF13646_consen 2 PALLQLLQNDPDPQVRAEAARALGELG----------DPEAIPALIELL------KDE-D-PMVRRAAARALGRIGDPEA 63 (88)
T ss_dssp HHHHHHHHTSSSHHHHHHHHHHHHCCT----------HHHHHHHHHHHH------TSS-S-HHHHHHHHHHHHCCHHHHT
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHcC----------CHhHHHHHHHHH------cCC-C-HHHHHHHHHHHHHhCCHHH
Confidence 4567777 8999999999999888442 225566666554 221 1 2233333333346899999
Q ss_pred HHHhhcccccchHHH-HHHHHHHHh
Q psy10447 140 INRVVDDLKDENEQY-RKMVMESIE 163 (166)
Q Consensus 140 l~~iv~~lKDesE~~-R~M~~eti~ 163 (166)
++.|..-++|++... |..+++++.
T Consensus 64 ~~~L~~~l~~~~~~~vr~~a~~aL~ 88 (88)
T PF13646_consen 64 IPALIKLLQDDDDEVVREAAAEALG 88 (88)
T ss_dssp HHHHHHHHTC-SSHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCcHHHHHHHHhhcC
Confidence 999999998876665 999998873
No 8
>PF12460 MMS19_C: RNAPII transcription regulator C-terminal; InterPro: IPR024687 This domain, approximately 60 amino acids in length, is found in the N-terminal region of MMS19 proteins. MMS19 is required for both nucleotide excision repair (NER) and RNA polymerase II (RNAP II) transcription [].
Probab=93.97 E-value=0.41 Score=42.66 Aligned_cols=78 Identities=17% Similarity=0.228 Sum_probs=68.5
Q ss_pred hhhhhhhHHHHHHHHhhhcchHHHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhccc
Q psy10447 12 ESFDSVLKPLWKGIRTHRGKGLAAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATD 89 (166)
Q Consensus 12 EsFd~VL~plW~Gir~hRGK~LAaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~ 89 (166)
.-|..++.+|=+|.+.+.+-.=..||.|+++|++-+-.+--.=+-.+++++|..-.+.||.+-+...|.+++......
T Consensus 319 R~F~~~~p~L~~~~~~~~~~~k~~yL~ALs~ll~~vP~~vl~~~l~~LlPLLlqsL~~~~~~v~~s~L~tL~~~l~~~ 396 (415)
T PF12460_consen 319 RFFTQVLPKLLEGFKEADDEIKSNYLTALSHLLKNVPKSVLLPELPTLLPLLLQSLSLPDADVLLSSLETLKMILEEA 396 (415)
T ss_pred HHHHHHHHHHHHHHhhcChhhHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHcC
Confidence 358888889988999988877788999999999998877666678889999999999999999999999999877665
No 9
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=91.21 E-value=0.57 Score=31.50 Aligned_cols=45 Identities=20% Similarity=0.343 Sum_probs=38.0
Q ss_pred hHHHHHHHHHHHhhCHHHHHHHhhcccccchHHHHHHHHHHHhhc
Q psy10447 121 RQLVDTTVEIANKVGASEIINRVVDDLKDENEQYRKMVMESIEKT 165 (166)
Q Consensus 121 ~~vv~TTv~lA~Kvg~~~il~~iv~~lKDesE~~R~M~~eti~kv 165 (166)
..+-...+....+.|..+++..|+.-++|++..-|+.++.++.++
T Consensus 14 ~~vr~~a~~~L~~~~~~~~~~~L~~~l~d~~~~vr~~a~~aL~~i 58 (88)
T PF13646_consen 14 PQVRAEAARALGELGDPEAIPALIELLKDEDPMVRRAAARALGRI 58 (88)
T ss_dssp HHHHHHHHHHHHCCTHHHHHHHHHHHHTSSSHHHHHHHHHHHHCC
T ss_pred HHHHHHHHHHHHHcCCHhHHHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence 344455566666899999999999999999999999999999875
No 10
>PF12719 Cnd3: Nuclear condensing complex subunits, C-term domain
Probab=90.55 E-value=1.1 Score=38.12 Aligned_cols=93 Identities=26% Similarity=0.327 Sum_probs=64.9
Q ss_pred HHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhHhhhhchHHHHHHHHHHhhhh
Q psy10447 37 LKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFKNFWNHRMALD 116 (166)
Q Consensus 37 LKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~FW~rR~AlD 116 (166)
++|+|. .-|.|.+.|.-|..-++..+ +.-+++.|-+.|+++-....+-|... +...--++
T Consensus 48 l~cLGl-~~Lld~~~a~~~l~l~~~~~----~~~~~~v~~~al~~l~Dll~~~g~~~--~~~~~~~~------------- 107 (298)
T PF12719_consen 48 LKCLGL-CCLLDKELAKEHLPLFLQAL----QKDDEEVKITALKALFDLLLTHGIDI--FDSESDND------------- 107 (298)
T ss_pred HHHHHH-HHHhChHHHHHHHHHHHHHH----HhCCHHHHHHHHHHHHHHHHHcCchh--ccchhccC-------------
Confidence 788885 46779888776665555544 44599999999999999988888553 32222222
Q ss_pred hhhhhHHHHHHHHHHHhhCHHHHHHHhhcccccchHHHHHHHHHHHhh
Q psy10447 117 RRNYRQLVDTTVEIANKVGASEIINRVVDDLKDENEQYRKMVMESIEK 164 (166)
Q Consensus 117 r~~~~~vv~TTv~lA~Kvg~~~il~~iv~~lKDesE~~R~M~~eti~k 164 (166)
...+...+++-+...++++++..|-.++|.+-|
T Consensus 108 ---------------~~~~~~~l~~~l~~~l~~~~~~~~~~a~EGl~K 140 (298)
T PF12719_consen 108 ---------------ESVDSKSLLKILTKFLDSENPELQAIAVEGLCK 140 (298)
T ss_pred ---------------ccchHhHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence 556666667777777777777777777777765
No 11
>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=90.27 E-value=4.5 Score=37.37 Aligned_cols=146 Identities=15% Similarity=0.195 Sum_probs=99.3
Q ss_pred hhhhhHHHHHHHHhhhcchHHHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcch
Q psy10447 14 FDSVLKPLWKGIRTHRGKGLAAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEA 93 (166)
Q Consensus 14 Fd~VL~plW~Gir~hRGK~LAaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~ 93 (166)
.......|..|+.+.--.+..--|+++|.++--=+.-..-.-..++.+.|..--.+||.+-.+...+++++++..+..-
T Consensus 75 ~~~~~~~L~~gL~h~~~~Vr~l~l~~l~~~~~~~~~~~~~~~~~~l~~~i~~~L~~~d~~Va~~A~~~L~~l~~~~~~~- 153 (503)
T PF10508_consen 75 LPQYQPFLQRGLTHPSPKVRRLALKQLGRIARHSEGAAQLLVDNELLPLIIQCLRDPDLSVAKAAIKALKKLASHPEGL- 153 (503)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCHHHHHHhcCccHHHHHHHHHcCCcHHHHHHHHHHHHHHhCCchhH-
Confidence 7778888999999988888888899998876322211222344678889999999999999999999999998765322
Q ss_pred hhHhhhhchHH-HHHHHHHHhhh-hhhhhhHHHHHHHHHHH-------hhCHHHHHHHhhcccccchHHHHHHHHHHHhh
Q psy10447 94 QYIKDEILPPF-FKNFWNHRMAL-DRRNYRQLVDTTVEIAN-------KVGASEIINRVVDDLKDENEQYRKMVMESIEK 164 (166)
Q Consensus 94 ~yir~~i~~~F-F~~FW~rR~Al-Dr~~~~~vv~TTv~lA~-------Kvg~~~il~~iv~~lKDesE~~R~M~~eti~k 164 (166)
+.++++- ....+.- ++- |-...-.+.+..++||. .+-.+.+++.++..|+|+.--.|.=++|.+..
T Consensus 154 ----~~l~~~~~~~~L~~l-~~~~~~~vR~Rv~el~v~i~~~S~~~~~~~~~sgll~~ll~eL~~dDiLvqlnalell~~ 228 (503)
T PF10508_consen 154 ----EQLFDSNLLSKLKSL-MSQSSDIVRCRVYELLVEIASHSPEAAEAVVNSGLLDLLLKELDSDDILVQLNALELLSE 228 (503)
T ss_pred ----HHHhCcchHHHHHHH-HhccCHHHHHHHHHHHHHHHhcCHHHHHHHHhccHHHHHHHHhcCccHHHHHHHHHHHHH
Confidence 2332322 2333321 111 21122234456666653 34444589999999999888889888888765
Q ss_pred c
Q psy10447 165 T 165 (166)
Q Consensus 165 v 165 (166)
+
T Consensus 229 L 229 (503)
T PF10508_consen 229 L 229 (503)
T ss_pred H
Confidence 3
No 12
>COG4748 Uncharacterized conserved protein [Function unknown]
Probab=88.20 E-value=0.74 Score=42.12 Aligned_cols=60 Identities=28% Similarity=0.407 Sum_probs=48.4
Q ss_pred hhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhHhhhhchHHHHHHHHHHhh
Q psy10447 53 NYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFKNFWNHRMA 114 (166)
Q Consensus 53 ~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~FW~rR~A 114 (166)
-.||+|+-.+|.+|++.|++|.=|-...=|.--..|-.+.-.| ..|+..=|+.|.+.|..
T Consensus 171 lkYt~eik~~la~e~~~Ps~Efvkffaa~v~~g~~t~~~~~kF--t~ivk~~~~qFi~D~vn 230 (365)
T COG4748 171 LKYTKEIKAYLAKETNNPSVEFVKFFAAKVYTGFKTTSVDEKF--TDIVKNAFSQFINDRVN 230 (365)
T ss_pred hhHHHHHHHHHHHhccCCCHHHHHHHHHHHhccceeeeHHHHH--HHHHHHHHHHHHHHHHH
Confidence 3699999999999999999999888877776555555565555 58888899999987753
No 13
>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=87.99 E-value=0.5 Score=27.74 Aligned_cols=27 Identities=15% Similarity=0.278 Sum_probs=22.6
Q ss_pred HHHHhhcccccchHHHHHHHHHHHhhc
Q psy10447 139 IINRVVDDLKDENEQYRKMVMESIEKT 165 (166)
Q Consensus 139 il~~iv~~lKDesE~~R~M~~eti~kv 165 (166)
++..+++-+.|+++.-|.+|++++.++
T Consensus 1 llp~l~~~l~D~~~~VR~~a~~~l~~i 27 (31)
T PF02985_consen 1 LLPILLQLLNDPSPEVRQAAAECLGAI 27 (31)
T ss_dssp HHHHHHHHHT-SSHHHHHHHHHHHHHH
T ss_pred CHHHHHHHcCCCCHHHHHHHHHHHHHH
Confidence 467788899999999999999998764
No 14
>PF10274 ParcG: Parkin co-regulated protein; InterPro: IPR019399 This family of proteins is transcribed anti-sense along the DNA to the Parkin gene product and the two appear to be transcribed under the same promoter. The protein has predicted alpha-helical and beta-sheet domains which suggest its function is in the ubiquitin/proteasome system []. Mutations in parkin are the genetic cause of early-onset and autosomal recessive juvenile parkinsonism.
Probab=86.28 E-value=2.8 Score=35.01 Aligned_cols=119 Identities=21% Similarity=0.438 Sum_probs=75.4
Q ss_pred hhhhhHHHHHHHHhhhc-------chHHHHHHH--HhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHh
Q psy10447 14 FDSVLKPLWKGIRTHRG-------KGLAAFLKA--IGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQ 84 (166)
Q Consensus 14 Fd~VL~plW~Gir~hRG-------K~LAaFLKa--iG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~q 84 (166)
|++.|--...|++.-.- +|..--|++ =.-|+|++ .+++.-|++-.+|.|.|-...+|+++++
T Consensus 36 y~~~Lpif~dGL~Et~~Py~flA~~g~~dll~~~~~~kilPvl---------PqLI~plk~AL~tr~~~V~~~~L~~Lq~ 106 (183)
T PF10274_consen 36 YHHYLPIFFDGLRETEHPYRFLARQGIKDLLERGGGEKILPVL---------PQLIIPLKRALNTRDPEVFCATLKALQQ 106 (183)
T ss_pred hhhHHHHHHhhhhccCccHHHHHHHHHHHHHHhcchhHHHHHH---------HHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 56777777777776211 111112222 22344543 4677779999999999999999999999
Q ss_pred hhccc-Ccchh---hHhhhhchHHHHHHHHHHh-h------hhhhhhhHHHHHHHHHHHhhCHHHHHHHh
Q psy10447 85 CCATD-GVEAQ---YIKDEILPPFFKNFWNHRM-A------LDRRNYRQLVDTTVEIANKVGASEIINRV 143 (166)
Q Consensus 85 c~~t~-gv~~~---yir~~i~~~FF~~FW~rR~-A------lDr~~~~~vv~TTv~lA~Kvg~~~il~~i 143 (166)
.+.+. +|.++ |.| .++| =|.-|=++|. - ..+++.+-+|+-|+++=++-|+.+-.-+|
T Consensus 107 Lv~~~~~vG~aLvPyyr-qLLp-~ln~f~~k~~n~gd~i~y~~~~~~~dlI~etL~~lE~~GG~dA~~nI 174 (183)
T PF10274_consen 107 LVTSSDMVGEALVPYYR-QLLP-VLNLFKNKNVNLGDGIDYRKRKNLGDLIQETLELLERNGGPDAFINI 174 (183)
T ss_pred HHHhhhhhhHHHHHHHH-HHHH-HHHHHHhcccCCCcccccccccchhHHHHHHHHHHHHhcChhHHHHH
Confidence 85543 33322 222 3443 3444555551 1 23468889999999999999998755443
No 15
>PTZ00429 beta-adaptin; Provisional
Probab=86.14 E-value=4.2 Score=40.17 Aligned_cols=96 Identities=15% Similarity=0.161 Sum_probs=61.4
Q ss_pred HHHHHHHhhcCCCcHHHHHHHHH-HHHhhhcccCcchhhHhhhhchHHHHHHHHHHhhhhhhhhhHHHH-HHHHHHH-hh
Q psy10447 58 EVMLILIREFQSPDEEMKKIVLK-VVKQCCATDGVEAQYIKDEILPPFFKNFWNHRMALDRRNYRQLVD-TTVEIAN-KV 134 (166)
Q Consensus 58 evm~il~rEF~SPDeEMKkiVLk-Vv~qc~~t~gv~~~yir~~i~~~FF~~FW~rR~AlDr~~~~~vv~-TTv~lA~-Kv 134 (166)
|+-. |..+++|+|++-||..|| |+.......-++. +--+|+. =++++.-..|++++ ....+|+ +-
T Consensus 33 e~~E-Lr~~L~s~~~~~kk~alKkvIa~mt~G~DvS~--LF~dVvk---------~~~S~d~elKKLvYLYL~~ya~~~p 100 (746)
T PTZ00429 33 EGAE-LQNDLNGTDSYRKKAAVKRIIANMTMGRDVSY--LFVDVVK---------LAPSTDLELKKLVYLYVLSTARLQP 100 (746)
T ss_pred hHHH-HHHHHHCCCHHHHHHHHHHHHHHHHCCCCchH--HHHHHHH---------HhCCCCHHHHHHHHHHHHHHcccCh
Confidence 5554 678889999887777765 6664444333333 2223332 23444445566663 3333444 33
Q ss_pred C-HHHHHHHhhcccccchHHHHHHHHHHHhhc
Q psy10447 135 G-ASEIINRVVDDLKDENEQYRKMVMESIEKT 165 (166)
Q Consensus 135 g-~~~il~~iv~~lKDesE~~R~M~~eti~kv 165 (166)
+ +.-++.-+..|++|.||..|-+|+.++..+
T Consensus 101 elalLaINtl~KDl~d~Np~IRaLALRtLs~I 132 (746)
T PTZ00429 101 EKALLAVNTFLQDTTNSSPVVRALAVRTMMCI 132 (746)
T ss_pred HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHcC
Confidence 3 345688999999999999999999998876
No 16
>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=83.47 E-value=4.7 Score=35.27 Aligned_cols=68 Identities=16% Similarity=0.145 Sum_probs=56.4
Q ss_pred hhhHHHHHHHH-hhhcc-----------hHHHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHH
Q psy10447 16 SVLKPLWKGIR-THRGK-----------GLAAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVK 83 (166)
Q Consensus 16 ~VL~plW~Gir-~hRGK-----------~LAaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~ 83 (166)
..|+-+|.... +.-|. ..+|=|.|-|+++.++++...+-+..+.++.|....+|+|-++|..-=..+-
T Consensus 174 ~~le~if~~~~~~~~~~~~~~~~~~~~~l~~aAL~aW~lLlt~~~~~~~~~~~~~~~~~l~~lL~s~d~~VRiAAGEaiA 253 (309)
T PF05004_consen 174 ESLESIFLLSILKSDGNAPVVAAEDDAALVAAALSAWALLLTTLPDSKLEDLLEEALPALSELLDSDDVDVRIAAGEAIA 253 (309)
T ss_pred HHHHHHHHHHhcCcCCCcccccCCCccHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHH
Confidence 67888898763 33333 6899999999999999998888888999999999999999999987655443
No 17
>KOG3961|consensus
Probab=82.70 E-value=1.8 Score=38.13 Aligned_cols=77 Identities=29% Similarity=0.444 Sum_probs=55.0
Q ss_pred HHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccC-cch----hhHhhhhchHHHHHHHHH-Hhhh-----hh-hhhhHHHH
Q psy10447 58 EVMLILIREFQSPDEEMKKIVLKVVKQCCATDG-VEA----QYIKDEILPPFFKNFWNH-RMAL-----DR-RNYRQLVD 125 (166)
Q Consensus 58 evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~g-v~~----~yir~~i~~~FF~~FW~r-R~Al-----Dr-~~~~~vv~ 125 (166)
++..-|++-|++-|+|.++.-|||++|.+.+.| |.+ =| | .++| -|.-|=+- ++.. || ++..-+++
T Consensus 155 qLI~plK~al~trd~ev~~~~Lkvlq~lv~~~~~vG~aLVPfY-R-QlLp-~~n~~k~~n~n~gd~idydk~~~igdlI~ 231 (262)
T KOG3961|consen 155 QLILPLKAALVTRDDEVICRTLKVLQQLVVSVGCVGAALVPFY-R-QLLP-VLNTFKNSNVNRGDGIDYDKNRNIGDLIN 231 (262)
T ss_pred HHHHHHHHHHhhccHHHHHHHHHHHHHHHHhccccchhhhhHH-H-Hhhh-hhhhhcccccccccccCccccccHHHHHH
Confidence 567779999999999999999999999999998 443 34 3 3443 34445443 3333 33 46677888
Q ss_pred HHHHHHHhhCHH
Q psy10447 126 TTVEIANKVGAS 137 (166)
Q Consensus 126 TTv~lA~Kvg~~ 137 (166)
-|.+.-+.-|+.
T Consensus 232 dTL~~LE~~GGp 243 (262)
T KOG3961|consen 232 DTLKHLERSGGP 243 (262)
T ss_pred HHHHHHHHcCCc
Confidence 888887777743
No 18
>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=81.99 E-value=25 Score=31.11 Aligned_cols=117 Identities=14% Similarity=0.286 Sum_probs=69.6
Q ss_pred HHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhHhhhhchHHHHHHHHHHhhhh
Q psy10447 37 LKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFKNFWNHRMALD 116 (166)
Q Consensus 37 LKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~FW~rR~AlD 116 (166)
+.++..| -.+++...-....+...|.+-..+|++-..-.+|+++.+++..+--.++ ...+++......=
T Consensus 173 ~~~l~~i--~~~~~~~~~~~~~~~~~L~~~l~~~~~~~q~~il~~l~~~~~~~~~~~~--~~~~i~~l~~~l~------- 241 (526)
T PF01602_consen 173 LSLLSEI--KCNDDSYKSLIPKLIRILCQLLSDPDPWLQIKILRLLRRYAPMEPEDAD--KNRIIEPLLNLLQ------- 241 (526)
T ss_dssp HHHHHHH--HCTHHHHTTHHHHHHHHHHHHHTCCSHHHHHHHHHHHTTSTSSSHHHHH--HHHHHHHHHHHHH-------
T ss_pred HHHHHHH--ccCcchhhhhHHHHHHHhhhcccccchHHHHHHHHHHHhcccCChhhhh--HHHHHHHHHHHhh-------
Confidence 4444444 2333332245555666666666899999999999999988765544441 0233333332221
Q ss_pred hhhhhHHH----HHHHHHHHhhC-HHHHHHHhhcccccchHHHHHHHHHHHhhc
Q psy10447 117 RRNYRQLV----DTTVEIANKVG-ASEIINRVVDDLKDENEQYRKMVMESIEKT 165 (166)
Q Consensus 117 r~~~~~vv----~TTv~lA~Kvg-~~~il~~iv~~lKDesE~~R~M~~eti~kv 165 (166)
.....|+ .+...++.... ...++..++..|.+.++..|-++++++..+
T Consensus 242 -s~~~~V~~e~~~~i~~l~~~~~~~~~~~~~L~~lL~s~~~nvr~~~L~~L~~l 294 (526)
T PF01602_consen 242 -SSSPSVVYEAIRLIIKLSPSPELLQKAINPLIKLLSSSDPNVRYIALDSLSQL 294 (526)
T ss_dssp -HHHHHHHHHHHHHHHHHSSSHHHHHHHHHHHHHHHTSSSHHHHHHHHHHHHHH
T ss_pred -ccccHHHHHHHHHHHHhhcchHHHHhhHHHHHHHhhcccchhehhHHHHHHHh
Confidence 2223333 33333333333 345678888889999999999999998764
No 19
>PF06575 DUF1132: Protein of unknown function (DUF1132); InterPro: IPR009509 This family consists of several hypothetical proteins from Neisseria meningitidis. The function of this family is unknown.
Probab=81.76 E-value=0.76 Score=35.18 Aligned_cols=18 Identities=28% Similarity=0.586 Sum_probs=15.0
Q ss_pred hhchHHHHHHHHHHhhhh
Q psy10447 99 EILPPFFKNFWNHRMALD 116 (166)
Q Consensus 99 ~i~~~FF~~FW~rR~AlD 116 (166)
..+-+-|.+|||||.+.|
T Consensus 35 ~~vie~fs~F~Nrri~~n 52 (95)
T PF06575_consen 35 FDVIECFSHFWNRRISNN 52 (95)
T ss_pred eeHHHHHHHHHHHHhhcC
Confidence 455689999999999876
No 20
>KOG1060|consensus
Probab=80.59 E-value=4.4 Score=41.21 Aligned_cols=68 Identities=18% Similarity=0.360 Sum_probs=55.4
Q ss_pred hHhhhhchHHHHHHHHHHhhhhhhhhhHHH-HHHHHHHHhhCHHHHHHHhhcccccchHHHHHHHHHHHhh
Q psy10447 95 YIKDEILPPFFKNFWNHRMALDRRNYRQLV-DTTVEIANKVGASEIINRVVDDLKDENEQYRKMVMESIEK 164 (166)
Q Consensus 95 yir~~i~~~FF~~FW~rR~AlDr~~~~~vv-~TTv~lA~Kvg~~~il~~iv~~lKDesE~~R~M~~eti~k 164 (166)
+-+..+..||||+|.+|- .|....+.+- +--.-||+--+.++|+..+-.+.|+..-.|=.|+++||.+
T Consensus 350 ~~~~~lF~P~lKsFfv~s--sDp~~vk~lKleiLs~La~esni~~ILrE~q~YI~s~d~~faa~aV~AiGr 418 (968)
T KOG1060|consen 350 IKRPTLFEPHLKSFFVRS--SDPTQVKILKLEILSNLANESNISEILRELQTYIKSSDRSFAAAAVKAIGR 418 (968)
T ss_pred hcchhhhhhhhhceEeec--CCHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHHhcCchhHHHHHHHHHHH
Confidence 347788999999999984 5655455444 5555689999999999999999999888899999999865
No 21
>PRK09687 putative lyase; Provisional
Probab=80.44 E-value=9.2 Score=32.90 Aligned_cols=32 Identities=19% Similarity=0.252 Sum_probs=18.2
Q ss_pred hhCHHHHHHHhhcccccchHHHHHHHHHHHhh
Q psy10447 133 KVGASEIINRVVDDLKDENEQYRKMVMESIEK 164 (166)
Q Consensus 133 Kvg~~~il~~iv~~lKDesE~~R~M~~eti~k 164 (166)
++|..+.++-|+.-|+|++...|..+++++.+
T Consensus 154 ~~~~~~ai~~L~~~L~d~~~~VR~~A~~aLg~ 185 (280)
T PRK09687 154 VINDEAAIPLLINLLKDPNGDVRNWAAFALNS 185 (280)
T ss_pred ccCCHHHHHHHHHHhcCCCHHHHHHHHHHHhc
Confidence 45555555555555556555555555555543
No 22
>PF01603 B56: Protein phosphatase 2A regulatory B subunit (B56 family); InterPro: IPR002554 Protein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that regulates multiple aspects of cell growth and metabolism. The ability of this widely distributed heterotrimeric enzyme to act on a diverse array of substrates is largely controlled by the nature of its regulatory B subunit. There are multiple families of B subunits, this family is called the B56 family [].; GO: 0008601 protein phosphatase type 2A regulator activity, 0007165 signal transduction, 0000159 protein phosphatase type 2A complex; PDB: 2NYM_B 2NYL_B 2IAE_E 2NPP_B 3FGA_B 2JAK_A.
Probab=80.43 E-value=5.2 Score=36.21 Aligned_cols=88 Identities=18% Similarity=0.332 Sum_probs=52.6
Q ss_pred hhhhhhhhHHHHHHHHhhhcchHHHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccC
Q psy10447 11 IESFDSVLKPLWKGIRTHRGKGLAAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDG 90 (166)
Q Consensus 11 IEsFd~VL~plW~Gir~hRGK~LAaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~g 90 (166)
-|.=+++++|-|.-+ .-+-.-|++-+-+ |-.|+ -..|-+...+.-|..-|+|||..-|..+.-++...-+.-.
T Consensus 93 ~~~d~~~~e~~WpHL----~~vY~il~~~i~~--~~~~~-~~~~i~~~fi~~Ll~l~~S~D~rER~~lk~~l~~iy~k~~ 165 (409)
T PF01603_consen 93 PDDDEPFLEPSWPHL----QLVYEILLRFIES--PPFDP-AKKYIDQKFIKKLLELFDSPDPRERDYLKTILHRIYGKFP 165 (409)
T ss_dssp GGG------TTHHHH----HHHHHHHHHHHTS--TT--C-CTTTS-HHHHHHHHHTTTSSTHHHHHHHHHHHHHHHHH-T
T ss_pred ccccccccccccHhH----HHHHHHHHHHHHC--ccccH-HHHHcCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhh
Confidence 344457999999843 3455555555444 33344 4558888999999999999999998877777766555544
Q ss_pred cchhhHhhhhchHHH
Q psy10447 91 VEAQYIKDEILPPFF 105 (166)
Q Consensus 91 v~~~yir~~i~~~FF 105 (166)
--..+||..|..-|.
T Consensus 166 ~~r~~Ir~~i~~~~~ 180 (409)
T PF01603_consen 166 NLRSFIRKSINNIFY 180 (409)
T ss_dssp TTHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHH
Confidence 455566666665554
No 23
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=78.96 E-value=16 Score=26.09 Aligned_cols=92 Identities=14% Similarity=0.266 Sum_probs=63.1
Q ss_pred cHHHHHHHHHHHHhhhcccCcchhhHhhhhchHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHhhCHH--HHHHHhhcccc
Q psy10447 71 DEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFKNFWNHRMALDRRNYRQLVDTTVEIANKVGAS--EIINRVVDDLK 148 (166)
Q Consensus 71 DeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~FW~rR~AlDr~~~~~vv~TTv~lA~Kvg~~--~il~~iv~~lK 148 (166)
+.++|..+..-+.+++..-++.+..+ ...=.+|..|..++. ..+.....+.-|.+-||.|+.-. --++.++.-.+
T Consensus 27 ~~~~r~~~~~~i~~~~~~~~l~~~~~--~~A~~~~dr~~~~~~-~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~ 103 (127)
T PF00134_consen 27 TPEMRQIIIDWIIELCQRLKLSPETL--HLAIYLFDRFLSKRP-VNRSKLQLIALACLFLASKMEEDNPPSISDLIRISD 103 (127)
T ss_dssp HHHHHHHHHHHHHHHHHHTT-BHHHH--HHHHHHHHHHHTTS--TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTT
T ss_pred CHHHHHHHHHHHHHHHHhcccchhHH--HHHHHHHHHHHhhcc-cccchhhhhhhhHHHHhhhhhccccchHHHHHHHHc
Confidence 46899999999999999999999987 444459999988774 55566777778999999998744 22455554442
Q ss_pred c--chHHHHHHHHHHHhhc
Q psy10447 149 D--ENEQYRKMVMESIEKT 165 (166)
Q Consensus 149 D--esE~~R~M~~eti~kv 165 (166)
+ ..+.+..|=.+-++.+
T Consensus 104 ~~~~~~~i~~~E~~iL~~L 122 (127)
T PF00134_consen 104 NTFTKKDILEMEREILSAL 122 (127)
T ss_dssp TSSHHHHHHHHHHHHHHHT
T ss_pred CCCCHHHHHHHHHHHHHHC
Confidence 2 3455555554444433
No 24
>PF01347 Vitellogenin_N: Lipoprotein amino terminal region; InterPro: IPR001747 This entry represents a conserved region found in several lipid transport proteins, including vitellogenin, microsomal triglyceride transfer protein and apolipoprotein B-100 []. Vitellinogen precursors provide the major egg yolk proteins that are a source of nutrients during early development of oviparous vertebrates and invertebrates. Vitellinogen precursors are multi-domain apolipoproteins that are cleaved into distinct yolk proteins. Different vitellinogen precursors exist, which are composed of variable combinations of yolk protein components; however, the cleavage sites are conserved. In vertebrates, a complete vitellinogen is composed of an N-terminal signal peptide for export, followed by four regions that can be cleaved into yolk proteins: lipovitellin-1, phosvitin, lipovitellin-2, and a von Willebrand factor type D domain (YGP40) [, ]. Microsomal triglyceride transfer protein (MTTP) is an endoplasmic reticulum lipid transfer protein involved in the biosynthesis and lipid loading of apolipoprotein B. MTTP is also involved in the late stage of CD1d trafficking in the lysosomal compartment, CD1d being the MHC I-like lipid antigen presenting molecule []. Apolipoprotein B can exist in two forms: B-100 and B-48. Apoliporotein B-100 is present on several lipoproteins, including very low-density lipoproteins (VLDL), intermediate density lipoproteins (IDL) and low density lipoproteins (LDL), and can assemble VLDL particles in the liver []. Apolipoprotein B-100 has been linked to the development of atherosclerosis.; GO: 0005319 lipid transporter activity, 0006869 lipid transport; PDB: 1LSH_A.
Probab=78.41 E-value=24 Score=32.49 Aligned_cols=91 Identities=13% Similarity=0.250 Sum_probs=53.7
Q ss_pred cHHHHHHHH----HHHHhhhccc------CcchhhHhhhhchHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHhhCHHHHH
Q psy10447 71 DEEMKKIVL----KVVKQCCATD------GVEAQYIKDEILPPFFKNFWNHRMALDRRNYRQLVDTTVEIANKVGASEII 140 (166)
Q Consensus 71 DeEMKkiVL----kVv~qc~~t~------gv~~~yir~~i~~~FF~~FW~rR~AlDr~~~~~vv~TTv~lA~Kvg~~~il 140 (166)
+...+.+.+ .++.++|... +-...-+.+++++.|.+.+= .|.++......+-.--.|.| +|...++
T Consensus 448 ~~~l~~ta~L~~~~lv~~~c~~~~~~~~~~~~~~~~~~~~~~~l~~~l~---~~~~~~~~~~~~~~LkaLgN-~g~~~~i 523 (618)
T PF01347_consen 448 SPYLRETALLSLGSLVHKYCVNSDSAEFCDPCSRCIIEKYVPYLEQELK---EAVSRGDEEEKIVYLKALGN-LGHPESI 523 (618)
T ss_dssp -HHHHHHHHHHHHHHHHHHHTT-----------SS--GGGTHHHHHHHH---HHHHTT-HHHHHHHHHHHHH-HT-GGGH
T ss_pred ChhHHHHHHHHHHHHhCceeecccccccccccchhhHHHHHHHHHHHHH---HHhhccCHHHHHHHHHHhhc-cCCchhh
Confidence 344555444 3466667662 11112234556665555432 55665554555545555776 8999999
Q ss_pred HHhhcccccc---hHHHHHHHHHHHhhc
Q psy10447 141 NRVVDDLKDE---NEQYRKMVMESIEKT 165 (166)
Q Consensus 141 ~~iv~~lKDe---sE~~R~M~~eti~kv 165 (166)
..++..+.++ +...|-.|+.|+.++
T Consensus 524 ~~l~~~i~~~~~~~~~~R~~Ai~Alr~~ 551 (618)
T PF01347_consen 524 PVLLPYIEGKEEVPHFIRVAAIQALRRL 551 (618)
T ss_dssp HHHHTTSTTSS-S-HHHHHHHHHTTTTG
T ss_pred HHHHhHhhhccccchHHHHHHHHHHHHH
Confidence 9999999988 888999999998754
No 25
>KOG1243|consensus
Probab=77.66 E-value=5.4 Score=39.53 Aligned_cols=77 Identities=21% Similarity=0.444 Sum_probs=60.5
Q ss_pred hHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhHhhhhchHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHhh
Q psy10447 55 YTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFKNFWNHRMALDRRNYRQLVDTTVEIANKV 134 (166)
Q Consensus 55 Yt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~FW~rR~AlDr~~~~~vv~TTv~lA~Kv 134 (166)
|-+.+++.|..=|.+||.-+|-..|.=+.|.+ +-++++-+.+.|+|.|=.+|=- .|.....+-+.+-..||-|+
T Consensus 327 yq~~i~p~l~kLF~~~Dr~iR~~LL~~i~~~i--~~Lt~~~~~d~I~phv~~G~~D----Tn~~Lre~Tlksm~~La~kL 400 (690)
T KOG1243|consen 327 YQVRIIPVLLKLFKSPDRQIRLLLLQYIEKYI--DHLTKQILNDQIFPHVALGFLD----TNATLREQTLKSMAVLAPKL 400 (690)
T ss_pred cccchhhhHHHHhcCcchHHHHHHHHhHHHHh--hhcCHHhhcchhHHHHHhhccc----CCHHHHHHHHHHHHHHHhhh
Confidence 99999999999999999999999999999776 5688888899999999888721 11223333445556788888
Q ss_pred CHH
Q psy10447 135 GAS 137 (166)
Q Consensus 135 g~~ 137 (166)
|-.
T Consensus 401 ~~~ 403 (690)
T KOG1243|consen 401 SKR 403 (690)
T ss_pred chh
Confidence 876
No 26
>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=74.62 E-value=19 Score=22.74 Aligned_cols=48 Identities=23% Similarity=0.183 Sum_probs=36.8
Q ss_pred HHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHH
Q psy10447 35 AFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVK 83 (166)
Q Consensus 35 aFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~ 83 (166)
+-+.|||.+. ---++....|..++++.|..-.++++++.|..-..-+.
T Consensus 6 ~A~~aLg~l~-~~~~~~~~~~~~~~~~~L~~~L~d~~~~VR~~A~~aLg 53 (55)
T PF13513_consen 6 AAAWALGRLA-EGCPELLQPYLPELLPALIPLLQDDDDSVRAAAAWALG 53 (55)
T ss_dssp HHHHHHHCTT-TTTHHHHHHHHHHHHHHHHHHTTSSSHHHHHHHHHHHH
T ss_pred HHHHHHhhHh-cccHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 3467899832 12467788899999999999999999988877665543
No 27
>PRK09687 putative lyase; Provisional
Probab=73.99 E-value=29 Score=29.82 Aligned_cols=90 Identities=9% Similarity=0.102 Sum_probs=60.9
Q ss_pred HHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhHhhhhchHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHhhC
Q psy10447 56 TKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFKNFWNHRMALDRRNYRQLVDTTVEIANKVG 135 (166)
Q Consensus 56 t~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~FW~rR~AlDr~~~~~vv~TTv~lA~Kvg 135 (166)
+.++...|+.-.+.+|++.|+....-+.++-..+.| |. |-+.+=.+ . . -+.+ ++-.-.+|
T Consensus 190 ~~~~~~~L~~~L~D~~~~VR~~A~~aLg~~~~~~av-~~-Li~~L~~~--------------~-~--~~~a-~~ALg~ig 249 (280)
T PRK09687 190 NPDIREAFVAMLQDKNEEIRIEAIIGLALRKDKRVL-SV-LIKELKKG--------------T-V--GDLI-IEAAGELG 249 (280)
T ss_pred CHHHHHHHHHHhcCCChHHHHHHHHHHHccCChhHH-HH-HHHHHcCC--------------c-h--HHHH-HHHHHhcC
Confidence 456777788888999999999999999876543322 22 21111110 0 0 1233 33344588
Q ss_pred HHHHHHHhhcccc-cchHHHHHHHHHHHhhc
Q psy10447 136 ASEIINRVVDDLK-DENEQYRKMVMESIEKT 165 (166)
Q Consensus 136 ~~~il~~iv~~lK-DesE~~R~M~~eti~kv 165 (166)
...-+..|..-++ +++...|+-++++++++
T Consensus 250 ~~~a~p~L~~l~~~~~d~~v~~~a~~a~~~~ 280 (280)
T PRK09687 250 DKTLLPVLDTLLYKFDDNEIITKAIDKLKRS 280 (280)
T ss_pred CHhHHHHHHHHHhhCCChhHHHHHHHHHhcC
Confidence 8899999999886 88999999999999874
No 28
>PF12755 Vac14_Fab1_bd: Vacuolar 14 Fab1-binding region
Probab=72.03 E-value=35 Score=25.23 Aligned_cols=72 Identities=24% Similarity=0.336 Sum_probs=50.6
Q ss_pred hHHHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhHhhhhchHHHHHHH-H
Q psy10447 32 GLAAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFKNFW-N 110 (166)
Q Consensus 32 ~LAaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~FW-~ 110 (166)
+||+.--++|. ...-|.+++++.+.+-|+.+|...|-....-+-+.+. . .++++++.|-+=|+ .
T Consensus 9 ~Laa~ai~l~~--------~~~~~l~~Il~pVL~~~~D~d~rVRy~AcEaL~ni~k------~-~~~~~l~~f~~IF~~L 73 (97)
T PF12755_consen 9 GLAAVAIALGK--------DISKYLDEILPPVLKCFDDQDSRVRYYACEALYNISK------V-ARGEILPYFNEIFDAL 73 (97)
T ss_pred HHHHHHHHchH--------hHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHHH------H-HHHHHHHHHHHHHHHH
Confidence 45555444443 3789999999999999999999999877665555432 2 37788874444454 5
Q ss_pred HHhhhhhh
Q psy10447 111 HRMALDRR 118 (166)
Q Consensus 111 rR~AlDr~ 118 (166)
-|...|..
T Consensus 74 ~kl~~D~d 81 (97)
T PF12755_consen 74 CKLSADPD 81 (97)
T ss_pred HHHHcCCc
Confidence 67777763
No 29
>PF10381 Autophagy_Cterm: Autophagocytosis associated protein C-terminal; InterPro: IPR019461 Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the vacuole. The small C-terminal domain is likely to be a distinct binding region for the stability of the autophagosome complex []. It carries a highly characteristic conserved FLKF sequence motif. ; PDB: 2DYT_A.
Probab=65.05 E-value=5.3 Score=23.97 Aligned_cols=19 Identities=42% Similarity=0.759 Sum_probs=14.6
Q ss_pred HHHHHHHHhhhcccCChhH
Q psy10447 33 LAAFLKAIGYLIPLMDAEY 51 (166)
Q Consensus 33 LAaFLKaiG~IIPLMD~ey 51 (166)
|--|||.+.++||-++=+|
T Consensus 5 l~iFLKFi~sViPtIeyD~ 23 (25)
T PF10381_consen 5 LVIFLKFISSVIPTIEYDY 23 (25)
T ss_dssp HHHHHHHHHHHSTTB--TT
T ss_pred ehhHHHHHhhcCCceeeec
Confidence 5569999999999987554
No 30
>TIGR00207 fliG flagellar motor switch protein FliG. The fliG protein along with fliM and fliN interact to form the switch complex of the bacterial flagellar motor located at the base of the basal body. This complex interacts with chemotaxis proteins (eg CHEY). In addition the complex interacts with other components of the motor that determine the direction of flagellar rotation. The model contains putative members of the fliG family at scores of less than 100 from Agrobacterium radiobacter and Sinorhizobium meliloti as well as fliG-like genes from treponema pallidum and Borrelia burgdorferi. That is why the suggested cutoff is set at 20 but was set at 100 to construct the family.
Probab=63.61 E-value=48 Score=29.50 Aligned_cols=76 Identities=14% Similarity=0.320 Sum_probs=55.3
Q ss_pred HHHHHHHHhhhcchHHHHHHH-----HhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcch
Q psy10447 19 KPLWKGIRTHRGKGLAAFLKA-----IGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEA 93 (166)
Q Consensus 19 ~plW~Gir~hRGK~LAaFLKa-----iG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~ 93 (166)
.|.|.-++.--.+.||.||+. +..|.--|+|+.|...- ..| |+++...++.++ ...++|+|
T Consensus 109 ~~~~~~L~~~~~~~la~~l~~EhPQ~iAliLs~L~p~~AA~VL--------~~L--p~~~~~ei~~ri----a~l~~vs~ 174 (338)
T TIGR00207 109 APGFEFLRKAEPQQIADFIQQEHPQTIALILSHLDPAQAADIL--------SLF--PEEVQAEVARRI----ATMGRTSP 174 (338)
T ss_pred CchhHHHHCCCHHHHHHHHHccCHHHHHHHHHcCCHHHHHHHH--------HhC--CHHHHHHHHHHH----HhcCCCCH
Confidence 357999999999999999974 77888889999987522 223 556666555555 45888999
Q ss_pred hhHhh--hhchHHHHHH
Q psy10447 94 QYIKD--EILPPFFKNF 108 (166)
Q Consensus 94 ~yir~--~i~~~FF~~F 108 (166)
+-+++ +++..|+...
T Consensus 175 ~~i~~ie~~L~~~~~~~ 191 (338)
T TIGR00207 175 EVVAEVERVLEGKLDSL 191 (338)
T ss_pred HHHHHHHHHHHHHHHhh
Confidence 88755 4777777654
No 31
>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=63.06 E-value=31 Score=23.45 Aligned_cols=69 Identities=14% Similarity=0.092 Sum_probs=40.8
Q ss_pred hhHHHHHHHHhhhcchHHHHHHHHhhhcccCChhHHhh-hHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhh
Q psy10447 17 VLKPLWKGIRTHRGKGLAAFLKAIGYLIPLMDAEYANY-YTKEVMLILIREFQSPDEEMKKIVLKVVKQCC 86 (166)
Q Consensus 17 VL~plW~Gir~hRGK~LAaFLKaiG~IIPLMD~eyA~y-Yt~evm~il~rEF~SPDeEMKkiVLkVv~qc~ 86 (166)
++++|-+-+...--+....-+.|++.|--- .++.... ....+++.|.+-.+++|.+.++..+-++.+++
T Consensus 50 ~i~~l~~~l~~~~~~v~~~a~~~L~~l~~~-~~~~~~~~~~~g~l~~l~~~l~~~~~~~~~~a~~~l~~l~ 119 (120)
T cd00020 50 GLPALVQLLKSEDEEVVKAALWALRNLAAG-PEDNKLIVLEAGGVPKLVNLLDSSNEDIQKNATGALSNLA 119 (120)
T ss_pred ChHHHHHHHhCCCHHHHHHHHHHHHHHccC-cHHHHHHHHHCCChHHHHHHHhcCCHHHHHHHHHHHHHhh
Confidence 333333333332234445556666666432 2233333 34457888888888888888888888887765
No 32
>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=62.53 E-value=11 Score=23.86 Aligned_cols=31 Identities=13% Similarity=0.231 Sum_probs=26.7
Q ss_pred CHHHHHHHhhcccccchHHHHHHHHHHHhhc
Q psy10447 135 GASEIINRVVDDLKDENEQYRKMVMESIEKT 165 (166)
Q Consensus 135 g~~~il~~iv~~lKDesE~~R~M~~eti~kv 165 (166)
-..+++..|+.-|+|+++.-|.-+..|+.++
T Consensus 25 ~~~~~~~~L~~~L~d~~~~VR~~A~~aLg~l 55 (55)
T PF13513_consen 25 YLPELLPALIPLLQDDDDSVRAAAAWALGNL 55 (55)
T ss_dssp HHHHHHHHHHHHTTSSSHHHHHHHHHHHHCH
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHhcC
Confidence 4567899999999999999999999998764
No 33
>PF04914 DltD_C: DltD C-terminal region; InterPro: IPR006998 The dlt operon (dltA to dltD) of Lactobacillus rhamnosus 7469 encodes four proteins responsible for the esterification of lipoteichoic acid (LTA) by D-alanine. These esters play an important role in controlling the net anionic charge of the poly (GroP) moiety of LTA. DltA and DltC encode the D-alanine-D-alanyl carrier protein ligase (Dcl) and D-alanyl carrier protein (Dcp), respectively. Whereas the functions of DltA and DltC are defined, the functions of DltB and DltD are unknown. In vitro assays showed that DltD bound Dcp for ligation with D-alanine by Dcl in the presence of ATP. In contrast, the homologue of Dcp, the Escherichia coli acyl carrier protein (ACP), involved in fatty acid biosynthesis, was not bound to DltD and thus was not ligated with D-alanine. DltD also catalyzed the hydrolysis of the mischarged D-alanyl-ACP. The hydrophobic N-terminal sequence of DltD was required for anchoring the protein in the membrane. It is hypothesized that this membrane-associated DltD facilitates the binding of Dcp and Dcl for ligation of Dcp with D-alanine and that the resulting D-alanyl-Dcp is translocated to the primary site of D-alanylation []. These sequences contain the C-terminal region of DltD.; PDB: 3BMA_C.
Probab=62.11 E-value=7.5 Score=30.56 Aligned_cols=73 Identities=22% Similarity=0.416 Sum_probs=48.1
Q ss_pred CCCcHHHHHHHHHHHHhhhcccCcchhhHhhhhchHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHhhCHHHHHHHhhccc
Q psy10447 68 QSPDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFKNFWNHRMALDRRNYRQLVDTTVEIANKVGASEIINRVVDDL 147 (166)
Q Consensus 68 ~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~FW~rR~AlDr~~~~~vv~TTv~lA~Kvg~~~il~~iv~~l 147 (166)
+||+=+==+.+|.+ |...|+.|-+ |++| ...-|..-+-+++.......+..-++++.-|+ ++++.-
T Consensus 31 ~SpEy~Dl~l~L~~----~k~~g~~~lf----Vi~P-vNg~wydytG~~~~~r~~~y~kI~~~~~~~gf-----~v~D~s 96 (130)
T PF04914_consen 31 KSPEYDDLQLLLDV----CKELGIDVLF----VIQP-VNGKWYDYTGLSKEMRQEYYKKIKYQLKSQGF-----NVADFS 96 (130)
T ss_dssp S-THHHHHHHHHHH----HHHTT-EEEE----EE-----HHHHHHTT--HHHHHHHHHHHHHHHHTTT-------EEE-T
T ss_pred CCccHHHHHHHHHH----HHHcCCceEE----EecC-CcHHHHHHhCCCHHHHHHHHHHHHHHHHHCCC-----EEEecc
Confidence 35544433444444 5567999976 3554 58899999999999999999999999999998 678888
Q ss_pred ccchHHH
Q psy10447 148 KDENEQY 154 (166)
Q Consensus 148 KDesE~~ 154 (166)
++|.|||
T Consensus 97 ~~~y~~y 103 (130)
T PF04914_consen 97 DDEYEPY 103 (130)
T ss_dssp TGTTSTT
T ss_pred cCCCCCc
Confidence 8888886
No 34
>cd07920 Pumilio Pumilio-family RNA binding domain. Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canon
Probab=61.51 E-value=37 Score=28.30 Aligned_cols=21 Identities=10% Similarity=0.317 Sum_probs=9.5
Q ss_pred HHHHHHHHhhCHHHHHHHhhc
Q psy10447 125 DTTVEIANKVGASEIINRVVD 145 (166)
Q Consensus 125 ~TTv~lA~Kvg~~~il~~iv~ 145 (166)
+....|++.--+..|+++++.
T Consensus 190 ~~~~~L~~d~~Gn~vvq~~l~ 210 (322)
T cd07920 190 EHALELVQDQFGNYVVQHVLE 210 (322)
T ss_pred HHHHHHhcCCchhhHHHHHHh
Confidence 333444444444445555443
No 35
>KOG3666|consensus
Probab=60.39 E-value=30 Score=35.54 Aligned_cols=53 Identities=38% Similarity=0.540 Sum_probs=45.4
Q ss_pred chHHHHHH-HHhhhcccC------Chh---HHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHH
Q psy10447 31 KGLAAFLK-AIGYLIPLM------DAE---YANYYTKEVMLILIREFQSPDEEMKKIVLKVVK 83 (166)
Q Consensus 31 K~LAaFLK-aiG~IIPLM------D~e---yA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~ 83 (166)
+.-|-||| |+..=.||| ||+ -||||+-|+..-|.+-.++--|-|=-|.+||+.
T Consensus 566 ~iRa~FlKLas~l~~pllrinqa~s~DlVsvsNyYS~eL~~~Lr~VLQiVPe~mF~Il~kiI~ 628 (1141)
T KOG3666|consen 566 KLRATFLKLASALDLPLLRINQANSPDLVSVSNYYSGELVSYLRKVLQIVPESMFTILLKIIK 628 (1141)
T ss_pred HHHHHHHHHHHHhhhHHHHhccCCCcchhhhhhHhhHHHHHHHHHHHHhchHHHHHHHHHHHh
Confidence 45578998 455568999 454 499999999999999999999999999999998
No 36
>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=59.65 E-value=86 Score=24.80 Aligned_cols=102 Identities=16% Similarity=0.267 Sum_probs=55.8
Q ss_pred HHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhHhhhhchHHHHHHHHHHhhhhhh-hhhHHHHHHHHHHHhhC-
Q psy10447 58 EVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFKNFWNHRMALDRR-NYRQLVDTTVEIANKVG- 135 (166)
Q Consensus 58 evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~FW~rR~AlDr~-~~~~vv~TTv~lA~Kvg- 135 (166)
+++..+....+|..--.=+.-+.+++.+...-|-.-+-.-+.++|+.++ +.+.-++ ......+|...|.+.++
T Consensus 53 ~~~~~i~~~l~d~Rs~v~~~A~~~l~~l~~~l~~~~~~~~~~~l~~Ll~-----~~~~~~~~i~~~a~~~L~~i~~~~~~ 127 (228)
T PF12348_consen 53 QLLDAIIKQLSDLRSKVSKTACQLLSDLARQLGSHFEPYADILLPPLLK-----KLGDSKKFIREAANNALDAIIESCSY 127 (228)
T ss_dssp ---HHHHH-S-HH---HHHHHHHHHHHHHHHHGGGGHHHHHHHHHHHHH-----GGG---HHHHHHHHHHHHHHHTTS-H
T ss_pred HhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHH-----HHccccHHHHHHHHHHHHHHHHHCCc
Confidence 5566777777766665666666666666544332221112444554443 3343333 33444477788999999
Q ss_pred HHHH-HHHhhcccccchHHHHHHHHHHHhh
Q psy10447 136 ASEI-INRVVDDLKDENEQYRKMVMESIEK 164 (166)
Q Consensus 136 ~~~i-l~~iv~~lKDesE~~R~M~~eti~k 164 (166)
...+ +..+...+++.|..-|.-+++.+..
T Consensus 128 ~~~~~~~~l~~~~~~Kn~~vR~~~~~~l~~ 157 (228)
T PF12348_consen 128 SPKILLEILSQGLKSKNPQVREECAEWLAI 157 (228)
T ss_dssp --HHHHHHHHHHTT-S-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 5677 8888889999999999999987754
No 37
>COG5096 Vesicle coat complex, various subunits [Intracellular trafficking and secretion]
Probab=59.14 E-value=34 Score=34.39 Aligned_cols=50 Identities=14% Similarity=0.211 Sum_probs=24.6
Q ss_pred HHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccC
Q psy10447 38 KAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDG 90 (166)
Q Consensus 38 KaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~g 90 (166)
-|+=.||--|-. +++-.++.+=+++.-.|-|-|.||.+---+.+|+...+
T Consensus 38 dAmK~iIa~M~~---G~dmssLf~dViK~~~trd~ElKrL~ylYl~~yak~~P 87 (757)
T COG5096 38 DAMKKIIAQMSL---GEDMSSLFPDVIKNVATRDVELKRLLYLYLERYAKLKP 87 (757)
T ss_pred HHHHHHHHHHhc---CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhccCH
Confidence 344445554421 11233444444444556666666666555555555444
No 38
>KOG4464|consensus
Probab=58.62 E-value=5.1 Score=38.32 Aligned_cols=83 Identities=22% Similarity=0.409 Sum_probs=55.6
Q ss_pred HHHHH---hhhcchHHHHHHHHhhhcccCCh------------------------------hHHh---hhHHHHHHHHHh
Q psy10447 22 WKGIR---THRGKGLAAFLKAIGYLIPLMDA------------------------------EYAN---YYTKEVMLILIR 65 (166)
Q Consensus 22 W~Gir---~hRGK~LAaFLKaiG~IIPLMD~------------------------------eyA~---yYt~evm~il~r 65 (166)
|++.+ .+..|.|+.-|+++-.+.|+=|. +-+. -|...-|.+|.+
T Consensus 234 ~k~~ke~~~~~~r~l~~llr~cl~~vT~~~~~~elhshav~~L~nv~~k~~~~~~~~~p~E~~sq~f~~~n~~~mdVi~~ 313 (532)
T KOG4464|consen 234 DKDVKEEHAIQARHLTILLRHCLLIVTLRDSTEELHSHAVNLLDNVPEKCLDVLAGAKPHECCSQCFEKRNGRNMDVILR 313 (532)
T ss_pred ccccchhhHHHHHHHHHHHHHHHhhccccchHHHHhhccCCccCCchhhhhhcccCCCCcchHHHHHHHhcchhHHHHHH
Confidence 66666 45667889999988888766441 1111 244445555443
Q ss_pred hcC---------CCcHHHHHHHHHHHHhhhcccCcchhhHhhhhchHH
Q psy10447 66 EFQ---------SPDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPF 104 (166)
Q Consensus 66 EF~---------SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~F 104 (166)
=.+ |.--|-=-=||.|+-.|+.++.+-.+|+|++|+||-
T Consensus 314 lLn~~~~qq~~~ss~~EllsPvlsVL~~car~~R~~Rkylr~qVLPPL 361 (532)
T KOG4464|consen 314 LLNFSEKQQEKESSLHELLSPVLSVLTECARSHRVMRKYLRQQVLPPL 361 (532)
T ss_pred HHHhhHHHHhhhhhhhhhhhhHHHHHHHHHhhhHHHHHHHHHhcCCch
Confidence 221 111223334999999999999999999999999996
No 39
>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=58.44 E-value=20 Score=20.75 Aligned_cols=28 Identities=14% Similarity=0.373 Sum_probs=23.3
Q ss_pred HHHHHHhhcCCCcHHHHHHHHHHHHhhh
Q psy10447 59 VMLILIREFQSPDEEMKKIVLKVVKQCC 86 (166)
Q Consensus 59 vm~il~rEF~SPDeEMKkiVLkVv~qc~ 86 (166)
+++.+..-+++|+++-|.....-+.+++
T Consensus 1 llp~l~~~l~D~~~~VR~~a~~~l~~i~ 28 (31)
T PF02985_consen 1 LLPILLQLLNDPSPEVRQAAAECLGAIA 28 (31)
T ss_dssp HHHHHHHHHT-SSHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHcCCCCHHHHHHHHHHHHHHH
Confidence 5788999999999999999988877665
No 40
>PF14664 RICTOR_N: Rapamycin-insensitive companion of mTOR, N-term
Probab=58.40 E-value=50 Score=29.87 Aligned_cols=97 Identities=13% Similarity=0.234 Sum_probs=64.8
Q ss_pred HHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhHhhhhchHHHHHHHHHHhh------hhhhhhhHHHHHHHHH--HHhh
Q psy10447 63 LIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFKNFWNHRMA------LDRRNYRQLVDTTVEI--ANKV 134 (166)
Q Consensus 63 l~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~FW~rR~A------lDr~~~~~vv~TTv~l--A~Kv 134 (166)
+..-+-+++-|+|-.-+|+++-+.....-...+.+-. ++ .|-+|-.. .+|.+.-++|-+-.++ +-+.
T Consensus 30 i~~~lL~~~~~vraa~yRilRy~i~d~~~l~~~~~l~-id----~~ii~SL~~~~~~~~ER~QALkliR~~l~~~~~~~~ 104 (371)
T PF14664_consen 30 IQCMLLSDSKEVRAAGYRILRYLISDEESLQILLKLH-ID----IFIIRSLDRDNKNDVEREQALKLIRAFLEIKKGPKE 104 (371)
T ss_pred HHHHHCCCcHHHHHHHHHHHHHHHcCHHHHHHHHHcC-Cc----hhhHhhhcccCCChHHHHHHHHHHHHHHHhcCCccc
Confidence 3336667779999999999999988776555543333 22 23344333 3444556667666666 2222
Q ss_pred CHHHHHHHhhcccccchHHHHHHHHHHHhh
Q psy10447 135 GASEIINRVVDDLKDENEQYRKMVMESIEK 164 (166)
Q Consensus 135 g~~~il~~iv~~lKDesE~~R~M~~eti~k 164 (166)
=..-|+..||.-.-++.++||.+++||+-.
T Consensus 105 ~~~~vvralvaiae~~~D~lr~~cletL~E 134 (371)
T PF14664_consen 105 IPRGVVRALVAIAEHEDDRLRRICLETLCE 134 (371)
T ss_pred CCHHHHHHHHHHHhCCchHHHHHHHHHHHH
Confidence 246677777777778999999999999854
No 41
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=58.29 E-value=9.5 Score=27.51 Aligned_cols=31 Identities=23% Similarity=0.330 Sum_probs=22.9
Q ss_pred CcHHHHHHHHHHHHh-hhcccCcchhhHhhhh
Q psy10447 70 PDEEMKKIVLKVVKQ-CCATDGVEAQYIKDEI 100 (166)
Q Consensus 70 PDeEMKkiVLkVv~q-c~~t~gv~~~yir~~i 100 (166)
--..+++.||.++++ |...+||..++|.+.+
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l 75 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQL 75 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHS
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHh
Confidence 356789999999999 9999999999886655
No 42
>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=56.79 E-value=1.5e+02 Score=27.54 Aligned_cols=124 Identities=11% Similarity=0.143 Sum_probs=85.4
Q ss_pred HHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhHhhhhchHHHHHHHHHHhh
Q psy10447 35 AFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFKNFWNHRMA 114 (166)
Q Consensus 35 aFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~FW~rR~A 114 (166)
.-..+++-++.-.+|... ....+..|.+=..+|++.-|.-+|+.|.+|......-.+ --.=++.+..-......
T Consensus 57 ~~~~iL~~~l~~~~~~~l---~~~~~~~L~~gL~h~~~~Vr~l~l~~l~~~~~~~~~~~~---~~~~~~l~~~i~~~L~~ 130 (503)
T PF10508_consen 57 LICDILKRLLSALSPDSL---LPQYQPFLQRGLTHPSPKVRRLALKQLGRIARHSEGAAQ---LLVDNELLPLIIQCLRD 130 (503)
T ss_pred HHHHHHHHHHhccCHHHH---HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCHHHHH---HhcCccHHHHHHHHHcC
Confidence 344677788877787775 666677788888899999999999999998865533221 11224556666666666
Q ss_pred hhhhhhhHHHHHHHHHHHh-hCHHHH-----HHHhhcccccchHHHHHHHHHHHhh
Q psy10447 115 LDRRNYRQLVDTTVEIANK-VGASEI-----INRVVDDLKDENEQYRKMVMESIEK 164 (166)
Q Consensus 115 lDr~~~~~vv~TTv~lA~K-vg~~~i-----l~~iv~~lKDesE~~R~M~~eti~k 164 (166)
-|-...+..+.+...||.. -|...+ +..|..-++.+|+.-|-=+.+.+-+
T Consensus 131 ~d~~Va~~A~~~L~~l~~~~~~~~~l~~~~~~~~L~~l~~~~~~~vR~Rv~el~v~ 186 (503)
T PF10508_consen 131 PDLSVAKAAIKALKKLASHPEGLEQLFDSNLLSKLKSLMSQSSDIVRCRVYELLVE 186 (503)
T ss_pred CcHHHHHHHHHHHHHHhCCchhHHHHhCcchHHHHHHHHhccCHHHHHHHHHHHHH
Confidence 6777777777777777743 344445 5677777777677777667776543
No 43
>PRK13800 putative oxidoreductase/HEAT repeat-containing protein; Provisional
Probab=56.50 E-value=53 Score=32.66 Aligned_cols=87 Identities=14% Similarity=0.149 Sum_probs=50.9
Q ss_pred HHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhHhhhhchHHHHHHH-HHHhhhhhhhhhHHHHHHHHHHHhhCHHHH
Q psy10447 61 LILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFKNFW-NHRMALDRRNYRQLVDTTVEIANKVGASEI 139 (166)
Q Consensus 61 ~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~FW-~rR~AlDr~~~~~vv~TTv~lA~Kvg~~~i 139 (166)
+.|.+=.+++|.+.|...+.-+.++...+.+.+. +...+-. .-| +|+.|.. .| .++|..+.
T Consensus 778 ~~L~~ll~D~d~~VR~aA~~aLg~~g~~~~~~~~-l~~aL~d----~d~~VR~~Aa~------------aL-~~l~~~~a 839 (897)
T PRK13800 778 DAVRALTGDPDPLVRAAALAALAELGCPPDDVAA-ATAALRA----SAWQVRQGAAR------------AL-AGAAADVA 839 (897)
T ss_pred HHHHHHhcCCCHHHHHHHHHHHHhcCCcchhHHH-HHHHhcC----CChHHHHHHHH------------HH-Hhccccch
Confidence 4455556677777777777777766544333211 2222211 234 3333222 12 34677777
Q ss_pred HHHhhcccccchHHHHHHHHHHHhhc
Q psy10447 140 INRVVDDLKDENEQYRKMVMESIEKT 165 (166)
Q Consensus 140 l~~iv~~lKDesE~~R~M~~eti~kv 165 (166)
+.-|+.-|+|+++.-|+.|+.++.++
T Consensus 840 ~~~L~~~L~D~~~~VR~~A~~aL~~~ 865 (897)
T PRK13800 840 VPALVEALTDPHLDVRKAAVLALTRW 865 (897)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHhcc
Confidence 78888888888888888888887654
No 44
>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=55.75 E-value=28 Score=19.98 Aligned_cols=28 Identities=21% Similarity=0.184 Sum_probs=22.7
Q ss_pred HHHHHHhhcCCCcHHHHHHHHHHHHhhh
Q psy10447 59 VMLILIREFQSPDEEMKKIVLKVVKQCC 86 (166)
Q Consensus 59 vm~il~rEF~SPDeEMKkiVLkVv~qc~ 86 (166)
.++.|+.-.+++|++.++..+..+.+.+
T Consensus 13 ~i~~L~~ll~~~~~~i~~~a~~aL~nl~ 40 (41)
T smart00185 13 GLPALVELLKSEDEEVVKEAAWALSNLS 40 (41)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 5666777777999999999999888764
No 45
>PF14631 FancD2: Fanconi anaemia protein FancD2 nuclease; PDB: 3S4W_B.
Probab=54.01 E-value=1.8e+02 Score=31.38 Aligned_cols=142 Identities=16% Similarity=0.235 Sum_probs=85.6
Q ss_pred hhhhHHHHHHHHhhhcchHHHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchh
Q psy10447 15 DSVLKPLWKGIRTHRGKGLAAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQ 94 (166)
Q Consensus 15 d~VL~plW~Gir~hRGK~LAaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~ 94 (166)
.-+++-|-.|+|.+ ...-.||+|+|..+-+-. +| .-..-+|-.+....++ .+||.+-+++++-+.+..++.+
T Consensus 345 ~lil~~lks~lr~~-k~l~eawiK~I~~~~~~~--~h--kv~Dl~lLlil~s~~~---~~~k~ie~ilkkKI~~g~it~~ 416 (1426)
T PF14631_consen 345 KLILDVLKSGLRFS-KDLSEAWIKAIESLEDAS--DH--KVIDLWLLLILYSINE---DNRKSIEKILKKKIKSGHITEQ 416 (1426)
T ss_dssp HHHHHHHHHHHHH--HHHHHHHHHHHHHGGGST--T----THHHHHHHHHHHH-H---HHHHHHHHHHHHHHTTT-S-HH
T ss_pred HHHHHHHHHHHHhc-cHHHHHHHHHHhcCCCcc--cc--chHHHHHHHHHHcCCc---cchHHHHHHHHHHHHhCcccHH
Confidence 35666677777654 467789999999996432 23 2356667777777655 7799999999999999998886
Q ss_pred hHh------hhhchHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHh----hCH---HHHHHHhhcccccchHHHHHHHHHH
Q psy10447 95 YIK------DEILPPFFKNFWNHRMALDRRNYRQLVDTTVEIANK----VGA---SEIINRVVDDLKDENEQYRKMVMES 161 (166)
Q Consensus 95 yir------~~i~~~FF~~FW~rR~AlDr~~~~~vv~TTv~lA~K----vg~---~~il~~iv~~lKDesE~~R~M~~et 161 (166)
.+. ..++.+||.++=.==-.+=|.....+++.-+++-.. ++. .+||+.||.+.=+.|++=-..|++.
T Consensus 417 ll~~~f~~~~~vL~~~f~siL~la~~Ll~S~e~~v~~FG~~~Y~~lF~~fds~~qqeVv~~Lvthi~sg~~~ev~~aL~v 496 (1426)
T PF14631_consen 417 LLDQTFKGHSEVLKDYFPSILSLAQSLLRSKEPSVREFGSHLYKYLFKEFDSYCQQEVVGALVTHIGSGNSQEVDAALDV 496 (1426)
T ss_dssp HHHHHHHHHHHHHTTSHHHHHHHHHHHHTSSSHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHHHHHHH--HHHHHHHHHH
T ss_pred HHHHHHhhhHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHcCCcHHHHHHHHHH
Confidence 653 356677777664211111133333444444433221 222 4788888888876677666777766
Q ss_pred Hhh
Q psy10447 162 IEK 164 (166)
Q Consensus 162 i~k 164 (166)
+.+
T Consensus 497 L~~ 499 (1426)
T PF14631_consen 497 LCE 499 (1426)
T ss_dssp HHH
T ss_pred HHH
Confidence 544
No 46
>KOG1232|consensus
Probab=53.63 E-value=15 Score=34.97 Aligned_cols=132 Identities=27% Similarity=0.403 Sum_probs=73.7
Q ss_pred ccCCcchhhhhhhhHHHHHHHHhhhcchHHHHHHHHhhhcccCCh---hHHhhhHHHHHHHHHhhc---------CC-Cc
Q psy10447 5 HCHTLSIESFDSVLKPLWKGIRTHRGKGLAAFLKAIGYLIPLMDA---EYANYYTKEVMLILIREF---------QS-PD 71 (166)
Q Consensus 5 as~PYGIEsFd~VL~plW~Gir~hRGK~LAaFLKaiG~IIPLMD~---eyA~yYt~evm~il~rEF---------~S-PD 71 (166)
+++=.||||||.|++- ....|++-|-.|+|| -|||. +-+--|.+.+-.-|..|+ .| -|
T Consensus 270 n~af~gi~sf~~v~k~-fv~Aks~L~EILSaf--------ElmD~~s~~~~~~~l~~l~~pl~~~~pFyiLiETsGSn~d 340 (511)
T KOG1232|consen 270 NVAFIGIESFDDVQKV-FVEAKSNLTEILSAF--------ELMDNASMELVLEYLKDLHFPLEDEHPFYILIETSGSNKD 340 (511)
T ss_pred eEEEEccccHHHHHHH-HHHHHHHHHHHHHHH--------HhhcchHHHHHHHHhccCCCCccCCCceEEEEEecCCCcc
Confidence 4566899999999975 566788888888887 35553 223333333322232222 22 22
Q ss_pred HH---HHHHHHHHHHhhhcccCcchhhHhhhhchHHHHHHHHHHhh----hhhh--hh--------hHHHHHHHHHHHhh
Q psy10447 72 EE---MKKIVLKVVKQCCATDGVEAQYIKDEILPPFFKNFWNHRMA----LDRR--NY--------RQLVDTTVEIANKV 134 (166)
Q Consensus 72 eE---MKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~FW~rR~A----lDr~--~~--------~~vv~TTv~lA~Kv 134 (166)
-| |---+...+.+-.-+|||-++=. .=++.+|..|-. +-+. .| +-+-+-+...-++.
T Consensus 341 hD~eKl~afl~d~lek~lIsDGv~a~d~------~~~~~lW~~Re~ip~a~~~~g~vyKyDvSLpL~d~Y~lvn~~~eRl 414 (511)
T KOG1232|consen 341 HDEEKLTAFLEDCLEKGLISDGVLAQDE------AEAQKLWKIRESIPEALQKAGGVYKYDVSLPLEDLYNLVNVMKERL 414 (511)
T ss_pred ccHHHHHHHHHHhhhhcccccceecCCH------HHHHHHHHHHhccHHHHHhcCCEEEeeccccHHHHHHHHHHHHHhh
Confidence 22 33345566666677888877642 347899977732 2110 01 11122233344567
Q ss_pred CHHHHHHHhhc--ccccch
Q psy10447 135 GASEIINRVVD--DLKDEN 151 (166)
Q Consensus 135 g~~~il~~iv~--~lKDes 151 (166)
|....+.+++. +|-|.|
T Consensus 415 ~~~~l~~d~~gyGHlGDgN 433 (511)
T KOG1232|consen 415 GEAALVGDIVGYGHLGDGN 433 (511)
T ss_pred hhhhhhhcccccccccCCc
Confidence 77777777664 355554
No 47
>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=52.73 E-value=33 Score=20.64 Aligned_cols=29 Identities=17% Similarity=0.208 Sum_probs=25.3
Q ss_pred HHHHHHHhhcCCCcHHHHHHHHHHHHhhh
Q psy10447 58 EVMLILIREFQSPDEEMKKIVLKVVKQCC 86 (166)
Q Consensus 58 evm~il~rEF~SPDeEMKkiVLkVv~qc~ 86 (166)
.+++.|++=..|+|+++++..+-.+.+++
T Consensus 12 g~i~~Lv~ll~~~~~~v~~~a~~al~nl~ 40 (41)
T PF00514_consen 12 GGIPPLVQLLKSPDPEVQEEAAWALGNLA 40 (41)
T ss_dssp THHHHHHHHTTSSSHHHHHHHHHHHHHHH
T ss_pred ccHHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 36788888899999999999999998875
No 48
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=52.11 E-value=49 Score=29.36 Aligned_cols=47 Identities=26% Similarity=0.424 Sum_probs=33.2
Q ss_pred HHHHHHHHHHhhhhhhhhhHHHHHHHHHHHhhCHHHH-HHHhhcccccc
Q psy10447 103 PFFKNFWNHRMALDRRNYRQLVDTTVEIANKVGASEI-INRVVDDLKDE 150 (166)
Q Consensus 103 ~FF~~FW~rR~AlDr~~~~~vv~TTv~lA~Kvg~~~i-l~~iv~~lKDe 150 (166)
-||+.||.+..-.+- .-+.+.-|.+-||-|+.-..+ +..++..++..
T Consensus 84 vyf~RFy~~~Sv~~~-~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~~~ 131 (305)
T TIGR00569 84 MYFKRFYLNNSVMEY-HPKIIMLTCVFLACKVEEFNVSIDQFVGNLKET 131 (305)
T ss_pred HHHhHHhccCchhhc-CHHHHHHHHHHHHHhccccCcCHHHHHhhccCC
Confidence 499999987766553 567777999999999874433 45555555443
No 49
>PF03224 V-ATPase_H_N: V-ATPase subunit H; InterPro: IPR004908 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 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: 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0000221 vacuolar proton-transporting V-type ATPase, V1 domain; PDB: 1HO8_A.
Probab=51.26 E-value=79 Score=27.04 Aligned_cols=138 Identities=13% Similarity=0.213 Sum_probs=64.8
Q ss_pred HHHHHHHhhhc--chHHHHHHHHhhhcc-----cCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcc
Q psy10447 20 PLWKGIRTHRG--KGLAAFLKAIGYLIP-----LMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVE 92 (166)
Q Consensus 20 plW~Gir~hRG--K~LAaFLKaiG~IIP-----LMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~ 92 (166)
|=|+|..+.+- ..=+.++|++-..-| ++ .+...-|.+-++.+|..- |++++..+-||-.+-.++..+.-.
T Consensus 15 i~W~~~~ra~~is~~~~~~ik~~~~~~~~~~~~~~-~~~~~~~~~~~l~lL~~~--~~~~d~v~yvL~li~dll~~~~~~ 91 (312)
T PF03224_consen 15 IPWDGYVRAGLISEEDLSLIKKLDKQSKEERRELL-EEDGDQYASLFLNLLNKL--SSNDDTVQYVLTLIDDLLSDDPSR 91 (312)
T ss_dssp --HHHHHHTTSS-HHHHHHHHHHHHHHH--------------------HHHHHH-----HHHHHHHHHHHHHHHH-SSSS
T ss_pred CCHHHHHHhCCCCHHHHHHHHHHHCCCHHHHHHHH-HhchhhHHHHHHHHHHHc--cCcHHHHHHHHHHHHHHHhcCHHH
Confidence 55777755432 233456666654433 22 233445666666666666 899999999999999998888755
Q ss_pred hhhHhh-------hhchHHHHHHHHHHhhhhhhhhhHHHHHHHHHHH---hhCH---HHHHHHhhccccc----chHHHH
Q psy10447 93 AQYIKD-------EILPPFFKNFWNHRMALDRRNYRQLVDTTVEIAN---KVGA---SEIINRVVDDLKD----ENEQYR 155 (166)
Q Consensus 93 ~~yir~-------~i~~~FF~~FW~rR~AlDr~~~~~vv~TTv~lA~---Kvg~---~~il~~iv~~lKD----esE~~R 155 (166)
.+.+.. ..+.|||+...+. |.....+-..--..|+. +-.. .+++..+++.+++ ++-+++
T Consensus 92 ~~~~~~~~~~~~~~~~~~fl~ll~~~----D~~i~~~a~~iLt~Ll~~~~~~~~~~~~~~l~~ll~~L~~~l~~~~~~~~ 167 (312)
T PF03224_consen 92 VELFLELAKQDDSDPYSPFLKLLDRN----DSFIQLKAAFILTSLLSQGPKRSEKLVKEALPKLLQWLSSQLSSSDSELQ 167 (312)
T ss_dssp HHHHHHHHH-TTH--HHHHHHH-S-S----SHHHHHHHHHHHHHHHTSTTT--HHHHHHHHHHHHHHHH-TT-HHHH---
T ss_pred HHHHHHhcccccchhHHHHHHHhcCC----CHHHHHHHHHHHHHHHHcCCccccchHHHHHHHHHHHHHHhhcCCCcchH
Confidence 555544 3667788754432 54333322222222221 1222 2677777777775 555667
Q ss_pred HHHHHHHhh
Q psy10447 156 KMVMESIEK 164 (166)
Q Consensus 156 ~M~~eti~k 164 (166)
.+++.++..
T Consensus 168 ~~av~~L~~ 176 (312)
T PF03224_consen 168 YIAVQCLQN 176 (312)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 777776653
No 50
>PF05002 SGS: SGS domain ; InterPro: IPR007699 This domain was thought to be unique to the SGT1-like proteins, but is also found in calcyclin binding proteins. Sgt1p is a highly conserved eukaryotic protein that is required for both SCF (Skp1p/Cdc53p-Cullin-F-box)-mediated ubiquitination and kinetochore function in yeast and also plays a role in the cAMP pathway. Calcyclin (S100A6) is a member of the S100A family of calcium binding proteins and appears to play a role in cell proliferation [].; PDB: 1X5M_A 2JTT_D.
Probab=50.13 E-value=13 Score=27.61 Aligned_cols=29 Identities=21% Similarity=0.440 Sum_probs=23.3
Q ss_pred HHHHHHhhcCCCcHHHHHHHHHHHHhhhc
Q psy10447 59 VMLILIREFQSPDEEMKKIVLKVVKQCCA 87 (166)
Q Consensus 59 vm~il~rEF~SPDeEMKkiVLkVv~qc~~ 87 (166)
+|..+..=|+.-||||||++.|-....-+
T Consensus 26 lm~lfkkiY~~gDDe~KRam~KSf~ES~G 54 (82)
T PF05002_consen 26 LMNLFKKIYDNGDDEMKRAMMKSFTESQG 54 (82)
T ss_dssp HHHHHHHHHTTS-SCHHHHHHHHHHCT--
T ss_pred HHHHHHHHHccCCHHHHHHHHHHHHHcCC
Confidence 89999999999999999999987765443
No 51
>PF12755 Vac14_Fab1_bd: Vacuolar 14 Fab1-binding region
Probab=49.64 E-value=45 Score=24.65 Aligned_cols=67 Identities=18% Similarity=0.231 Sum_probs=46.4
Q ss_pred hhhhhhhhHHHHHHHHhhhcchHHHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHH
Q psy10447 11 IESFDSVLKPLWKGIRTHRGKGLAAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIV 78 (166)
Q Consensus 11 IEsFd~VL~plW~Gir~hRGK~LAaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiV 78 (166)
-+.|+.+++|+-+...-+=-|+=-+=..|+..|.=..-.+.-. |..||...|.+-+..||+.-|..-
T Consensus 22 ~~~l~~Il~pVL~~~~D~d~rVRy~AcEaL~ni~k~~~~~~l~-~f~~IF~~L~kl~~D~d~~Vr~~a 88 (97)
T PF12755_consen 22 SKYLDEILPPVLKCFDDQDSRVRYYACEALYNISKVARGEILP-YFNEIFDALCKLSADPDENVRSAA 88 (97)
T ss_pred HHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHcCCchhHHHHH
Confidence 3568888888888876555554333445666664443333333 889999999999999999977654
No 52
>COG2947 Uncharacterized conserved protein [Function unknown]
Probab=49.56 E-value=5.9 Score=32.77 Aligned_cols=30 Identities=27% Similarity=0.651 Sum_probs=27.2
Q ss_pred CcchhhhhhhhHHHHHHHHhhhcchHHHHHHHH
Q psy10447 8 TLSIESFDSVLKPLWKGIRTHRGKGLAAFLKAI 40 (166)
Q Consensus 8 PYGIEsFd~VL~plW~Gir~hRGK~LAaFLKai 40 (166)
-||||....+-+-.|.|+|+++.+. |+++|
T Consensus 13 ~~s~~~l~~~g~~~W~GVRNYqARN---fmR~M 42 (156)
T COG2947 13 VFSIEMLKAVGEEPWDGVRNYQARN---FMRDM 42 (156)
T ss_pred cccHHHHHHhCcCcccchHHHHHHH---HHHhc
Confidence 3899999999999999999999998 88883
No 53
>KOG0212|consensus
Probab=49.29 E-value=52 Score=32.73 Aligned_cols=129 Identities=20% Similarity=0.269 Sum_probs=81.3
Q ss_pred HHHhhhcchHHHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcc--hhhHh--hh
Q psy10447 24 GIRTHRGKGLAAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVE--AQYIK--DE 99 (166)
Q Consensus 24 Gir~hRGK~LAaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~--~~yir--~~ 99 (166)
.||+.--..|..||+.|-+= | ++.=+.++.++++..-+||+++.+.+-|.-++..+...|=. +.+-. ..
T Consensus 223 eVr~~~~t~l~~fL~eI~s~-----P--~s~d~~~~i~vlv~~l~ss~~~iq~~al~Wi~efV~i~g~~~l~~~s~il~~ 295 (675)
T KOG0212|consen 223 EVRTLTDTLLSEFLAEIRSS-----P--SSMDYDDMINVLVPHLQSSEPEIQLKALTWIQEFVKIPGRDLLLYLSGILTA 295 (675)
T ss_pred HHHHHHHHHHHHHHHHHhcC-----c--cccCcccchhhccccccCCcHHHHHHHHHHHHHHhcCCCcchhhhhhhhhhh
Confidence 56666778899999999842 2 23356789999999999999999999999888877665521 21111 33
Q ss_pred hchHHHHHHHHHHh-h--hhhhhh---hHHHHHHHHHHHhhCHHHHHHHhhcccccchHHHHHHHHHHHh
Q psy10447 100 ILPPFFKNFWNHRM-A--LDRRNY---RQLVDTTVEIANKVGASEIINRVVDDLKDENEQYRKMVMESIE 163 (166)
Q Consensus 100 i~~~FF~~FW~rR~-A--lDr~~~---~~vv~TTv~lA~Kvg~~~il~~iv~~lKDesE~~R~M~~eti~ 163 (166)
|+|--=. +.-| + .+.-++ ..++.+-. +-+.++..-|++-+...++|++|.-|.-|++=|.
T Consensus 296 iLpc~s~---~e~~~i~~~a~~~n~~l~~l~s~~~-~~~~id~~~ii~vl~~~l~~~~~~tri~~L~Wi~ 361 (675)
T KOG0212|consen 296 ILPCLSD---TEEMSIKEYAQMVNGLLLKLVSSER-LKEEIDYGSIIEVLTKYLSDDREETRIAVLNWII 361 (675)
T ss_pred cccCCCC---CccccHHHHHHHHHHHHHHHHhhhh-hccccchHHHHHHHHHHhhcchHHHHHHHHHHHH
Confidence 4331000 0000 0 001111 11111111 2222777889999999999999999998887653
No 54
>TIGR01716 RGG_Cterm transcriptional activator, Rgg/GadR/MutR family, C-terminal domain. This model describes the whole, except for a 60 residue N-terminal helix-turn-helix DNA-binding domain (PFAM pfam01381) of the family of proteins related to the transcriptional regulator Rgg, also called RopB. Rgg is required for secretion of several proteins, including a cysteine proteinase associated with virulence. GadR is a positive regulator of a glutamate-dependent acid resistance mechanism. MutR is a transcriptional activator for mutacin biosynthesis genes in Streptococcus mutans. This family appears restricted to the low-GC Gram-positive bacteria, including at least eight members in Lactococcus lactis.
Probab=46.90 E-value=31 Score=27.26 Aligned_cols=49 Identities=16% Similarity=0.247 Sum_probs=36.8
Q ss_pred HHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhh
Q psy10447 36 FLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCC 86 (166)
Q Consensus 36 FLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~ 86 (166)
=|.-+|.+++++|++....+.+++..-..+--++| ..+..+..++-++.
T Consensus 87 eL~Lf~n~~~~l~~~~~~~l~~~il~~~~~~~~~~--~~~~~i~~il~N~~ 135 (220)
T TIGR01716 87 ELYLFGNTMSILNSEDLEFLGKELLERLKRYRELN--RYRRRVIQLLLNIA 135 (220)
T ss_pred HHHHHHhHHHHcCHHHHHHHHHHHHHhhhHHHhHh--hhHHHHHHHHHHHH
Confidence 57788999999999999999999987644332333 47777777776665
No 55
>smart00708 PhBP Insect pheromone/odorant binding protein domains.
Probab=46.70 E-value=69 Score=21.77 Aligned_cols=70 Identities=17% Similarity=0.334 Sum_probs=44.9
Q ss_pred chHHHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhHhhhhchHHHHHH
Q psy10447 31 KGLAAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFKNF 108 (166)
Q Consensus 31 K~LAaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~F 108 (166)
...--|++|+.--+=+||++ ..+-...++..+. . +++-...+..++.+|....+-..+. -+-.-.||+.|
T Consensus 30 ~~~kC~~~C~~~~~g~~~~~-g~~~~~~~~~~~~----~-~~~~~~~~~~~~~~C~~~~~~~~~~--Ce~a~~~~~C~ 99 (103)
T smart00708 30 EKVKCYIKCVLKKLGLVDDD-GKFDAEKLLEQLK----A-DDEMAEELEDIIEKCEKKKGTEEDP--CDTAYRVAKCF 99 (103)
T ss_pred cccCcHHHHHHHHcCCcCCC-CCcCHHHHHHHHH----c-ChhHHHHHHHHHHHHHhhcCCCCCc--hHHHHHHHHHH
Confidence 34455899999999999974 3455555554443 3 5666789999999998777643221 13333466554
No 56
>cd01042 DMQH Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain. Demethoxyubiquinone hydroxylases (DMQH) are members of the ferritin-like, diiron-carboxylate family which are present in eukaryotes (the CLK-1/CAT5 family) and prokaryotes (the Coq7 family). DMQH participates in one of the last steps of ubiquinone biosysnthesis and is responsible for DMQ hydroxylation, resulting in the formation of hydroxyubiquinone, a precursor of ubiquinone. CLK-1 is a mitochondrial inner membrane protein and Coq7 is a proposed interfacial integral membrane protein. Mutations in the Caenorhabditis elegans gene clk-1 affect biological timing and extend longevity. The conserved residues of a diiron center are present in this domain.
Probab=46.28 E-value=37 Score=27.77 Aligned_cols=43 Identities=33% Similarity=0.497 Sum_probs=30.3
Q ss_pred hhhHHHHHHHHhhhcchHHHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCC
Q psy10447 16 SVLKPLWKGIRTHRGKGLAAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQS 69 (166)
Q Consensus 16 ~VL~plW~Gir~hRGK~LAaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~S 69 (166)
++|.|||.. ++| ++|++=.||.++.+-.+|-+|=..+.+.+++
T Consensus 61 s~l~PlW~~---------~gf--~lG~~tal~G~~~a~~~~~avE~~V~~Hy~~ 103 (165)
T cd01042 61 SLLLPLWYV---------AGF--ALGALTALLGKKAAMACTAAVETVVEEHYND 103 (165)
T ss_pred chHHHHHHH---------HHH--HHHHHHHhhChHHHHHHHHHHHHHHHHHHHH
Confidence 567888853 333 4788888888888877777777776666554
No 57
>smart00638 LPD_N Lipoprotein N-terminal Domain.
Probab=46.16 E-value=1.9e+02 Score=26.62 Aligned_cols=49 Identities=12% Similarity=0.129 Sum_probs=32.5
Q ss_pred hhhhhhHHHHHHHHHHHhhCHHHHHHHhhcccc-cc--hHHHHHHHHHHHhhc
Q psy10447 116 DRRNYRQLVDTTVEIANKVGASEIINRVVDDLK-DE--NEQYRKMVMESIEKT 165 (166)
Q Consensus 116 Dr~~~~~vv~TTv~lA~Kvg~~~il~~iv~~lK-De--sE~~R~M~~eti~kv 165 (166)
+++.....+-..-.|+| .|...++..+...+. |+ +...|.+|+.|+.++
T Consensus 456 ~~~~~~~~~~~LkaLGN-~g~~~~i~~l~~~l~~~~~~~~~iR~~Av~Alr~~ 507 (574)
T smart00638 456 SKGDEEEIQLYLKALGN-AGHPSSIKVLEPYLEGAEPLSTFIRLAAILALRNL 507 (574)
T ss_pred hcCCchheeeHHHhhhc-cCChhHHHHHHHhcCCCCCCCHHHHHHHHHHHHHH
Confidence 33434333333344555 899999888888877 33 456899999998754
No 58
>PF09337 zf-H2C2: His(2)-Cys(2) zinc finger; InterPro: IPR015416 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents an H2C2-type zinc finger that binds to histone upstream activating sequence (UAS) elements found in histone gene promoters []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=45.72 E-value=15 Score=23.43 Aligned_cols=24 Identities=29% Similarity=0.564 Sum_probs=17.7
Q ss_pred HHhhcCCCcHHHHHHHHHHHHhhhcc
Q psy10447 63 LIREFQSPDEEMKKIVLKVVKQCCAT 88 (166)
Q Consensus 63 l~rEF~SPDeEMKkiVLkVv~qc~~t 88 (166)
|.+.|-=| -||+.|-++|++|...
T Consensus 15 i~~~y~W~--gm~~~V~~~ir~C~~C 38 (39)
T PF09337_consen 15 ISQRYHWP--GMKKDVRRVIRSCPQC 38 (39)
T ss_pred HHHhheec--CHHHHHHHHHhcCccc
Confidence 44444444 4999999999999864
No 59
>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=45.52 E-value=58 Score=23.79 Aligned_cols=53 Identities=19% Similarity=0.303 Sum_probs=33.3
Q ss_pred HHHHHHHHHhhcCCCcHH-----------HHHHHHHHHHhhhcccCcchhhHhhhhchHHHHHHHH
Q psy10447 56 TKEVMLILIREFQSPDEE-----------MKKIVLKVVKQCCATDGVEAQYIKDEILPPFFKNFWN 110 (166)
Q Consensus 56 t~evm~il~rEF~SPDeE-----------MKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~FW~ 110 (166)
+.+++.-|...|..|..+ .|..|+.++++-+..-.- ++-.+.-+-.++.+|++
T Consensus 42 p~~ll~~L~~rf~~~~~~~~~~~~~~~~~~~~rv~~~l~~Wv~~~~~--dF~~~~~l~~~l~~f~~ 105 (127)
T smart00229 42 TQELLQLLLYRYNAIPPESWVERKVNPLRVKNRVLNILRHWVENYWQ--DFEDDPKLILRLLEFLD 105 (127)
T ss_pred HHHHHHHHHHHhCCCCcHHHHHHHhhHHHHHHHHHHHHHHHHHHCCc--ccccCHHHHHHHHHHHH
Confidence 368888999999877655 566677777766655442 44323224456666664
No 60
>PF14500 MMS19_N: Dos2-interacting transcription regulator of RNA-Pol-II
Probab=44.81 E-value=77 Score=27.29 Aligned_cols=51 Identities=22% Similarity=0.493 Sum_probs=43.1
Q ss_pred hhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhHhhhhchHHHHHHHH
Q psy10447 53 NYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFKNFWN 110 (166)
Q Consensus 53 ~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~FW~ 110 (166)
..|..-.++.|.--..|+...-|.-+|+.+..|+.+=|. .-+.+|....|+
T Consensus 203 ~~fa~~~~p~LleKL~s~~~~~K~D~L~tL~~c~~~y~~-------~~~~~~~~~iw~ 253 (262)
T PF14500_consen 203 PLFAPFAFPLLLEKLDSTSPSVKLDSLQTLKACIENYGA-------DSLSPHWSTIWN 253 (262)
T ss_pred HhhHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHHHCCH-------HHHHHHHHHHHH
Confidence 566777899999999999999999999999999986653 334689999995
No 61
>PLN03200 cellulose synthase-interactive protein; Provisional
Probab=42.76 E-value=2e+02 Score=32.41 Aligned_cols=148 Identities=16% Similarity=0.190 Sum_probs=87.4
Q ss_pred hHHHHHHHHhhhcchHHHHHHHHhhhcccCChhHHhh---hHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhccc-Ccch
Q psy10447 18 LKPLWKGIRTHRGKGLAAFLKAIGYLIPLMDAEYANY---YTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATD-GVEA 93 (166)
Q Consensus 18 L~plW~Gir~hRGK~LAaFLKaiG~IIPLMD~eyA~y---Yt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~-gv~~ 93 (166)
+.|||.-+...=.+....-|+++|.|..+-+-+...- =+....+.|..=-+|++++.|+.-..++.+++.+. ++..
T Consensus 566 I~~Lv~LLlsdd~~~~~~aL~vLgnIlsl~~~~d~~~~g~~~~ggL~~Lv~LL~sgs~~ikk~Aa~iLsnL~a~~~d~~~ 645 (2102)
T PLN03200 566 ISQLTALLLGDLPESKVHVLDVLGHVLSVASLEDLVREGSAANDALRTLIQLLSSSKEETQEKAASVLADIFSSRQDLCE 645 (2102)
T ss_pred HHHHHHHhcCCChhHHHHHHHHHHHHHhhcchhHHHHHhhhccccHHHHHHHHcCCCHHHHHHHHHHHHHHhcCChHHHH
Confidence 3444443333333444445667777766554321000 01245677888888999999999999998887654 3333
Q ss_pred hhHhhhhchHHHHHHHHHHhhhhhhhhhHHHHHHH--HHHHhh--CHHHHHHHhhcccccchHHHHHHHHHHHhhc
Q psy10447 94 QYIKDEILPPFFKNFWNHRMALDRRNYRQLVDTTV--EIANKV--GASEIINRVVDDLKDENEQYRKMVMESIEKT 165 (166)
Q Consensus 94 ~yir~~i~~~FF~~FW~rR~AlDr~~~~~vv~TTv--~lA~Kv--g~~~il~~iv~~lKDesE~~R~M~~eti~kv 165 (166)
.-+....+||--..-++.....=+.-...+..-+. .=.|+. ....++.-|++.|++++...+..+++++..+
T Consensus 646 avv~agaIpPLV~LLss~~~~v~keAA~AL~nL~~~~~~~q~~~~v~~GaV~pL~~LL~~~d~~v~e~Al~ALanL 721 (2102)
T PLN03200 646 SLATDEIINPCIKLLTNNTEAVATQSARALAALSRSIKENRKVSYAAEDAIKPLIKLAKSSSIEVAEQAVCALANL 721 (2102)
T ss_pred HHHHcCCHHHHHHHHhcCChHHHHHHHHHHHHHHhCCCHHHHHHHHHcCCHHHHHHHHhCCChHHHHHHHHHHHHH
Confidence 44577888998887765332211111111111110 001222 2244677899999999999999999998653
No 62
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=41.93 E-value=57 Score=20.12 Aligned_cols=37 Identities=24% Similarity=0.398 Sum_probs=27.7
Q ss_pred HHHHhhCH-HHHHHHhhcccccchHHHHHHHHHHHhhc
Q psy10447 129 EIANKVGA-SEIINRVVDDLKDENEQYRKMVMESIEKT 165 (166)
Q Consensus 129 ~lA~Kvg~-~~il~~iv~~lKDesE~~R~M~~eti~kv 165 (166)
+||++.|. ..-+.++++.-..-+++.|..+.+++...
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~~vs~~~~~~i~~~~~~l 39 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEEL 39 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHh
Confidence 57888885 55778877765556888888888887764
No 63
>PF14561 TPR_20: Tetratricopeptide repeat; PDB: 3QOU_A 2R5S_A 3QDN_B.
Probab=41.93 E-value=33 Score=24.89 Aligned_cols=43 Identities=14% Similarity=0.342 Sum_probs=34.0
Q ss_pred HHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhHhhhh
Q psy10447 57 KEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIKDEI 100 (166)
Q Consensus 57 ~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i 100 (166)
..+..++.+.-..-|+.-||.+|.++..|-.++-++.+| |..+
T Consensus 43 ~~Ll~~v~~dr~~~~~~ar~~ll~~f~~lg~~~plv~~~-RRkL 85 (90)
T PF14561_consen 43 DQLLELVRRDRDYEDDAARKRLLDIFELLGPGDPLVSEY-RRKL 85 (90)
T ss_dssp HHHHHHHCC-TTCCCCHHHHHHHHHHHHH-TT-HHHHHH-HHHH
T ss_pred HHHHHHHHhCccccccHHHHHHHHHHHHcCCCChHHHHH-HHHH
Confidence 456777888888889999999999999999998899998 6554
No 64
>cd06561 AlkD_like A new structural DNA glycosylase. This domain represents a new and uncharacterized structural superfamily of DNA glycosylases that form an alpha-alpha superhelix fold that are not belong to the identified five structural DNA glycosylase superfamilies (UDG, AAG/MNPG, MutM/Fpg and helix-hairpin-helix). DNA glycosylases removing alkylated base residues have been identified in all organisms investigated and may be universally present in nature. DNA glycosylases catalyze the first step in Base Excision Repair (BER) pathway by cleaving damaged DNA bases within double strand DNA to produce an abasic site. The resulting abasic site is further processed by AP endonuclease, phosphodiesterase, DNA polymerases, and DNA ligase functions to restore the DNA to an undamaged state. All glycosylase examined to date utilize a similar strategy for binding DNA and base flipping despite their structural diversity.
Probab=41.49 E-value=55 Score=25.30 Aligned_cols=44 Identities=16% Similarity=0.345 Sum_probs=23.4
Q ss_pred HHHHHHhhhhhhhhhHHHHHHHHHHHhhCHHHHHHHhhcccccchHHHHHHHH
Q psy10447 107 NFWNHRMALDRRNYRQLVDTTVEIANKVGASEIINRVVDDLKDENEQYRKMVM 159 (166)
Q Consensus 107 ~FW~rR~AlDr~~~~~vv~TTv~lA~Kvg~~~il~~iv~~lKDesE~~R~M~~ 159 (166)
+.|.||.|. .+++....+-+..+-+-.++..++++.|.|=+|++
T Consensus 118 ~~~~rR~~~---------~~~~~~~~~~~~~~~~l~~~~~~~~d~~~~Vqkav 161 (197)
T cd06561 118 NEWVRRAAI---------VLLLRLIKKETDFDLLLEIIERLLHDEEYFVQKAV 161 (197)
T ss_pred cHHHHHHHH---------HHHHHHHHhcccHHHHHHHHHHhCCCHHHHHHHHH
Confidence 578888773 33344444433334444445555555566655554
No 65
>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=41.36 E-value=33 Score=22.77 Aligned_cols=22 Identities=18% Similarity=0.437 Sum_probs=16.4
Q ss_pred HHHhhcCCCcHHHHHHHHHHHH
Q psy10447 62 ILIREFQSPDEEMKKIVLKVVK 83 (166)
Q Consensus 62 il~rEF~SPDeEMKkiVLkVv~ 83 (166)
++..=+++.|+++++-+.||+.
T Consensus 34 ~~~~~~~~~~~~~~~kv~rll~ 55 (64)
T PF04818_consen 34 AFAHAYKNVDPEVRKKVQRLLN 55 (64)
T ss_dssp HHHHHCCCS-HHHHHHHHHHHH
T ss_pred HHHHHHhcCCHHHHHHHHHHHH
Confidence 4555566779999999999885
No 66
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=40.67 E-value=35 Score=21.11 Aligned_cols=27 Identities=33% Similarity=0.528 Sum_probs=18.6
Q ss_pred hHHHHHHHHhhhcccCChhHHhhhHHHH
Q psy10447 32 GLAAFLKAIGYLIPLMDAEYANYYTKEV 59 (166)
Q Consensus 32 ~LAaFLKaiG~IIPLMD~eyA~yYt~ev 59 (166)
.|..|||-||.+ ||+.++---.+.+.+
T Consensus 3 ~l~~Yl~ei~~~-~LLt~eeE~~LA~~i 29 (37)
T PF00140_consen 3 SLRLYLKEIGRY-PLLTAEEEIELARRI 29 (37)
T ss_dssp HHHHHHHHHHHS--EETTHHHHHHHHHH
T ss_pred HHHHHHHHHcCC-CCCCHHHHHHHHHHH
Confidence 367899999998 999876554444444
No 67
>PF06371 Drf_GBD: Diaphanous GTPase-binding Domain; InterPro: IPR010473 Diaphanous-related formins (Drfs) are a family of formin homology (FH) proteins that act as effectors of Rho small GTPases during growth factor-induced cytoskeletal remodelling, stress fibre formation, and cell division []. Drf proteins are characterised by a variety of shared domains: an N-terminal GTPase-binding domain (GBD), formin-homology domains FH1, FH2 (IPR003104 from INTERPRO) and FH3 (IPR010472 from INTERPRO), and a C-terminal conserved Dia-autoregulatory domain (DAD) that binds the GBD. This entry represents the GBD, which is a bifunctional autoinhibitory domain that interacts with and is regulated by activated Rho family members. Mammalian Drf3 contains a CRIB-like motif within its GBD for binding to Cdc42, which is required for Cdc42 to activate and guide Drf3 towards the cell cortex where it remodels the actin skeleton [].; GO: 0003779 actin binding, 0017048 Rho GTPase binding, 0030036 actin cytoskeleton organization; PDB: 3OBV_A 2BNX_A 3EG5_D 2BAP_B 3O4X_B 1Z2C_B 2F31_A.
Probab=40.67 E-value=62 Score=24.79 Aligned_cols=52 Identities=17% Similarity=0.390 Sum_probs=34.6
Q ss_pred hHHHHHHHHhhhcccCChhHH-h--hhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhh
Q psy10447 32 GLAAFLKAIGYLIPLMDAEYA-N--YYTKEVMLILIREFQSPDEEMKKIVLKVVKQCC 86 (166)
Q Consensus 32 ~LAaFLKaiG~IIPLMD~eyA-~--yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~ 86 (166)
....+|+|+=.| |+-.+. . .-..+.+..|.+-+.||+...|+.||.++.-.|
T Consensus 132 ~~~~~l~Clkal---~n~~~G~~~v~~~~~~v~~i~~~L~s~~~~~r~~~leiL~~lc 186 (187)
T PF06371_consen 132 IEHECLRCLKAL---MNTKYGLEAVLSHPDSVNLIALSLDSPNIKTRKLALEILAALC 186 (187)
T ss_dssp HHHHHHHHHHHH---TSSHHHHHHHHCSSSHHHHHHHT--TTSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH---HccHHHHHHHHcCcHHHHHHHHHHCCCCHHHHHHHHHHHHHHH
Confidence 456667776554 553331 1 113456788999999999999999999987665
No 68
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=38.60 E-value=1.9e+02 Score=22.68 Aligned_cols=85 Identities=16% Similarity=0.240 Sum_probs=51.0
Q ss_pred HHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhHhhhh------------------chHHHHHHHHHHhhhhhhhh
Q psy10447 59 VMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIKDEI------------------LPPFFKNFWNHRMALDRRNY 120 (166)
Q Consensus 59 vm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i------------------~~~FF~~FW~rR~AlDr~~~ 120 (166)
.++.+..-+++||+..|+..|.++.++...+=+-. |..+ ..-||..++..+ -....+
T Consensus 26 ~~~~l~~~L~D~~~~VR~~al~~Ls~Li~~d~ik~---k~~l~~~~l~~l~D~~~~Ir~~A~~~~~e~~~~~--~~~~i~ 100 (178)
T PF12717_consen 26 YLPNLYKCLRDEDPLVRKTALLVLSHLILEDMIKV---KGQLFSRILKLLVDENPEIRSLARSFFSELLKKR--NPNIIY 100 (178)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCceee---hhhhhHHHHHHHcCCCHHHHHHHHHHHHHHHHhc--cchHHH
Confidence 34556677889999999999999999987654433 2222 233555555443 112245
Q ss_pred hHHHHHHHHHHHhhC-----------HHHHHHHhhcccc
Q psy10447 121 RQLVDTTVEIANKVG-----------ASEIINRVVDDLK 148 (166)
Q Consensus 121 ~~vv~TTv~lA~Kvg-----------~~~il~~iv~~lK 148 (166)
..+++.-..|++--+ ...|...++++++
T Consensus 101 ~~~~e~i~~l~~~~~~~~~~~~~~~~~~~I~~fll~~i~ 139 (178)
T PF12717_consen 101 NNFPELISSLNNCYEHPVYGPLSREKRKKIYKFLLDFID 139 (178)
T ss_pred HHHHHHHHHHhCccccccccccCHHHHHHHHHHHHHHcC
Confidence 555566555655221 2456666666666
No 69
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=37.92 E-value=1.1e+02 Score=19.47 Aligned_cols=81 Identities=12% Similarity=0.157 Sum_probs=49.7
Q ss_pred HHHHHHHHhhhcccCcchhhHhhhhchHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHhhCHH-HHHHHhhccccc-chHH
Q psy10447 76 KIVLKVVKQCCATDGVEAQYIKDEILPPFFKNFWNHRMALDRRNYRQLVDTTVEIANKVGAS-EIINRVVDDLKD-ENEQ 153 (166)
Q Consensus 76 kiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~FW~rR~AlDr~~~~~vv~TTv~lA~Kvg~~-~il~~iv~~lKD-esE~ 153 (166)
.....-+.+++..-+..++-. .+.-.+|+.|=.. ...++.+...+.-|.+-||.|+.-. .-+..++..... .-+.
T Consensus 3 ~~~~~~l~~~~~~~~~~~~~~--~~A~~~~~~~~~~-~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~ 79 (88)
T cd00043 3 PTPLDFLRRVAKALGLSPETL--TLAVNLLDRFLLD-YSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYATEEE 79 (88)
T ss_pred chHHHHHHHHHHHcCCCHHHH--HHHHHHHHHHHHh-cccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCCCHHH
Confidence 344455566666667776643 4444566666443 3345778888889999999998433 445555555555 5555
Q ss_pred HHHHHH
Q psy10447 154 YRKMVM 159 (166)
Q Consensus 154 ~R~M~~ 159 (166)
+++|..
T Consensus 80 i~~~e~ 85 (88)
T cd00043 80 ILRMEK 85 (88)
T ss_pred HHHHHH
Confidence 555544
No 70
>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=37.45 E-value=19 Score=27.90 Aligned_cols=46 Identities=28% Similarity=0.473 Sum_probs=37.3
Q ss_pred CCccccCCcchhhhhhhhHHHHHHHHhhhcchHHHHHHHHhhhcccC
Q psy10447 1 MTDIHCHTLSIESFDSVLKPLWKGIRTHRGKGLAAFLKAIGYLIPLM 47 (166)
Q Consensus 1 ~~~~as~PYGIEsFd~VL~plW~Gir~hRGK~LAaFLKaiG~IIPLM 47 (166)
|.+||.+-|--+.|..|++-||+-+..+ ||.=-.-+||+--|==|+
T Consensus 22 m~eIa~~t~~~~~~~~Im~~l~kRL~~~-~k~WR~vyKaL~lleyLl 67 (123)
T cd03571 22 MAEIARATYNYVEFQEIMSMLWKRLNDK-GKNWRHVYKALTLLEYLL 67 (123)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHHHHHhc-cccHHHHHHHHHHHHHHH
Confidence 4567777888889999999999999988 888888888887663333
No 71
>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....
Probab=37.43 E-value=57 Score=20.66 Aligned_cols=30 Identities=23% Similarity=0.520 Sum_probs=22.6
Q ss_pred hhhhhhhHHHHHHHHhhh-cch--HHHHHHHHh
Q psy10447 12 ESFDSVLKPLWKGIRTHR-GKG--LAAFLKAIG 41 (166)
Q Consensus 12 EsFd~VL~plW~Gir~hR-GK~--LAaFLKaiG 41 (166)
|....++--+|+.+.+++ +++ +.+||..+.
T Consensus 25 D~~qe~~~~l~~~~~~~~~~~~~~~~~~l~~~~ 57 (71)
T PF04542_consen 25 DLVQEAFIKLWRAIDSYDPDRGDSFRAWLFRIA 57 (71)
T ss_dssp HHHHHHHHHHHHHHHHTSTTSSSHHHHHHHHHH
T ss_pred HHhhHHHHHHHhhhhcccccccCCHHHHHHHHH
Confidence 456677888999999887 666 888887653
No 72
>cd07920 Pumilio Pumilio-family RNA binding domain. Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canon
Probab=36.66 E-value=1.8e+02 Score=24.25 Aligned_cols=33 Identities=21% Similarity=0.322 Sum_probs=20.5
Q ss_pred HHHHHhhCHHHHHHHhhcccccchHHHHHHHHHHHh
Q psy10447 128 VEIANKVGASEIINRVVDDLKDENEQYRKMVMESIE 163 (166)
Q Consensus 128 v~lA~Kvg~~~il~~iv~~lKDesE~~R~M~~eti~ 163 (166)
.+||+--=+..|+++++.... +..|+..++.+.
T Consensus 271 ~~l~~d~~Gn~Viq~~l~~~~---~~~~~~i~~~l~ 303 (322)
T cd07920 271 DTLMKDQYGNYVIQTALDVAK---EEQRELLVEAIR 303 (322)
T ss_pred HHHhCCCcccHHHHHHHHhCC---HHHHHHHHHHHH
Confidence 456665566677777776666 245666665554
No 73
>PRK06922 hypothetical protein; Provisional
Probab=36.03 E-value=79 Score=31.53 Aligned_cols=72 Identities=26% Similarity=0.447 Sum_probs=48.6
Q ss_pred cccCCh--------hHHhhhHHHHHHHHHhhcCC--------------CcHHHH---------HHHHHHHHhhhcccCcc
Q psy10447 44 IPLMDA--------EYANYYTKEVMLILIREFQS--------------PDEEMK---------KIVLKVVKQCCATDGVE 92 (166)
Q Consensus 44 IPLMD~--------eyA~yYt~evm~il~rEF~S--------------PDeEMK---------kiVLkVv~qc~~t~gv~ 92 (166)
=|||+. -|-|-|++.+..-..||..+ |||.|+ ..-.+++.-|+..+.+.
T Consensus 290 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~ 369 (677)
T PRK06922 290 EKLMQQLHYDFKGEKKDNVYRKRVIEKYLREYRENEKPNTTHVSFQVKVDEDMKTAYVSFRFSAVGEALITFCVEAEKID 369 (677)
T ss_pred HHHHHHHHHhhcCcchhhHHHHHHHHHHHHHhcccCCCCCcceeeeeccccccceeeEEEeecHHHHHHHHHHHhhhhcc
Confidence 488864 34577999998888887653 567773 23478999999999999
Q ss_pred hhhHhhhhchHHHHHHHHHHhhhhh
Q psy10447 93 AQYIKDEILPPFFKNFWNHRMALDR 117 (166)
Q Consensus 93 ~~yir~~i~~~FF~~FW~rR~AlDr 117 (166)
|-|-|..++ +|..|=.|.-+.||
T Consensus 370 ~~~~r~~~~--~fd~fg~r~D~~dR 392 (677)
T PRK06922 370 MMHARANVL--LFDFFGLRKDAYDR 392 (677)
T ss_pred hHHHHHHhH--HHHHhccChhhHhH
Confidence 999665543 45444333223343
No 74
>PF12765 Cohesin_HEAT: HEAT repeat associated with sister chromatid cohesion
Probab=35.91 E-value=42 Score=21.27 Aligned_cols=28 Identities=14% Similarity=0.382 Sum_probs=23.8
Q ss_pred CHHHHHHHhhcccccchHHHHHHHHHHH
Q psy10447 135 GASEIINRVVDDLKDENEQYRKMVMESI 162 (166)
Q Consensus 135 g~~~il~~iv~~lKDesE~~R~M~~eti 162 (166)
+...|..-|...|.|++..-|+-|++.|
T Consensus 15 ~~~~v~~~i~~rl~D~s~~VR~aav~ll 42 (42)
T PF12765_consen 15 DSSDVQSAIIRRLSDSSPSVREAAVDLL 42 (42)
T ss_pred chHHHHHHHHHHhcCCChHHHHHHHHHC
Confidence 3457888888899999999999999874
No 75
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=35.73 E-value=59 Score=21.19 Aligned_cols=40 Identities=25% Similarity=0.420 Sum_probs=34.0
Q ss_pred HHHHHHhhCHH-HHHHHhhcccccchHHHHHHHHHHHhhcC
Q psy10447 127 TVEIANKVGAS-EIINRVVDDLKDENEQYRKMVMESIEKTN 166 (166)
Q Consensus 127 Tv~lA~Kvg~~-~il~~iv~~lKDesE~~R~M~~eti~kv~ 166 (166)
--+||+..|++ --+.+.++.-..=|+.-|.-+++++++++
T Consensus 2 i~dIA~~agvS~~TVSr~ln~~~~vs~~tr~rI~~~a~~lg 42 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVLNGPPRVSEETRERILEAAEELG 42 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHHTTCSSSTHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHC
Confidence 45788998875 46899999889999999999999998864
No 76
>PF08064 UME: UME (NUC010) domain; InterPro: IPR012993 This domain is characteristic of UVSB PI-3 kinase, MEI-41 and ESR1 [].; GO: 0004674 protein serine/threonine kinase activity
Probab=35.54 E-value=75 Score=23.60 Aligned_cols=47 Identities=19% Similarity=0.251 Sum_probs=40.0
Q ss_pred HHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHh
Q psy10447 35 AFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQ 84 (166)
Q Consensus 35 aFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~q 84 (166)
.-|+|||.+|= |-..|.+-+.-.||..|.--...| |++...+++-.-
T Consensus 34 ~~l~si~~lI~-~~~~~i~~~~pQI~a~L~sal~~~--~l~~~al~~W~~ 80 (107)
T PF08064_consen 34 RALRSIEELIK-LGGSHISSARPQIMACLQSALEIP--ELREEALSCWNC 80 (107)
T ss_pred HHHHHHHHHHH-HhHHHHHHHHHHHHHHHHHHhCCh--hhHHHHHHHHHH
Confidence 36889999999 788999999999999999988888 888887776553
No 77
>PF08623 TIP120: TATA-binding protein interacting (TIP20); InterPro: IPR013932 TIP120 (also known as cullin-associated and neddylation-dissociated protein 1) is a TATA binding protein interacting protein that enhances transcription []. ; PDB: 4A0C_A 1U6G_C.
Probab=35.36 E-value=52 Score=27.10 Aligned_cols=33 Identities=24% Similarity=0.350 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHhh-hcccCcchhhHhhhhchHHHHHHHHH
Q psy10447 72 EEMKKIVLKVVKQC-CATDGVEAQYIKDEILPPFFKNFWNH 111 (166)
Q Consensus 72 eEMKkiVLkVv~qc-~~t~gv~~~yir~~i~~~FF~~FW~r 111 (166)
+|+.|.+||++..+ -..+|....- +-|..||..
T Consensus 132 ~E~~rs~lr~~~~l~~~i~~~~~~~-------~~~~~f~~~ 165 (169)
T PF08623_consen 132 QELIRSVLRAVKALNSKIPGAESSP-------NKWNEFVEW 165 (169)
T ss_dssp HHHHHHHHHHHHHH-HSSTS-SSSH--------HHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhCcccccCH-------HHHHHHHHH
Confidence 68999999999987 4444443321 578888853
No 78
>PF13877 RPAP3_C: Potential Monad-binding region of RPAP3
Probab=34.98 E-value=69 Score=22.70 Aligned_cols=67 Identities=15% Similarity=0.343 Sum_probs=40.7
Q ss_pred HHHHHHHHhhhcchHHHHHHHHhhh-cc-cCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhccc
Q psy10447 19 KPLWKGIRTHRGKGLAAFLKAIGYL-IP-LMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATD 89 (166)
Q Consensus 19 ~plW~Gir~hRGK~LAaFLKaiG~I-IP-LMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~ 89 (166)
+-.|+.++. .....+.||+.|+-= +| |...+-..-.-.+++.+|...+.+.|.+ .|+.++++.+.+.
T Consensus 11 ~~~w~~~~~-~~~~~~~yL~~i~p~~l~~if~~~l~~~~L~~il~~l~~~~~~~~~~---~i~~~L~~L~~~~ 79 (94)
T PF13877_consen 11 ERDWRRLKK-DPEERYEYLKSIPPDSLPKIFKNSLEPEFLSEILEALNEHFIPEDPE---FIFEILEALSKVK 79 (94)
T ss_pred HHHHHHHcC-CHHHHHHHHHhCChHHHHHHHHccCCHHHHHHHHHHHHHHHccCCHH---HHHHHHHHhcCCC
Confidence 346888863 455889999987421 11 1111222334567777777777766665 7777777766554
No 79
>PF08389 Xpo1: Exportin 1-like protein; InterPro: IPR013598 The exchange of macromolecules between the nucleus and cytoplasm takes place through nuclear pore complexes within the nuclear membrane. Active transport of large molecules through these pore complexes require carrier proteins, called karyopherins (importins and exportins), which shuttle between the two compartments. This domain is found close to the N terminus of yeast exportin 1 (Xpo1, Crm1, P14068 from SWISSPROT), as well as adjacent to the N-terminal domain of importin-beta (IPR001494 from INTERPRO). Exportin 1 is a nuclear export receptor that translocates proteins out of the nucleus; it interacts with leucine-rich nuclear export signal (NES) sequences in proteins to be transported, as well as with RanGTP [, ]. Importin-beta is a nuclear import receptor that translocates proteins into the nucleus; it interacts with RanGTP and importin-alpha, the latter binding with the nuclear localisation signal (NLS) sequences in proteins to be transported []. More information about these proteins can be found at Protein of the Month: Importins [].; PDB: 3IBV_A 3ICQ_U 3M1I_C 3NC1_A 3NBY_D 3NBZ_D 3NC0_A 3GJX_D 2XWU_B 2X19_B ....
Probab=34.97 E-value=1.1e+02 Score=22.11 Aligned_cols=57 Identities=18% Similarity=0.213 Sum_probs=37.9
Q ss_pred hhhhhhHHHHHHHHhhh----cchHHHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCc
Q psy10447 13 SFDSVLKPLWKGIRTHR----GKGLAAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPD 71 (166)
Q Consensus 13 sFd~VL~plW~Gir~hR----GK~LAaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPD 71 (166)
.+..|++-+.+.+..+- .....+-|+|+++.++-+|+++-.= ..++..+.+=.++|+
T Consensus 79 ~~~~i~~~l~~~l~~~~~~~~~~~~~~~L~~l~s~i~~~~~~~i~~--~~~l~~~~~~l~~~~ 139 (148)
T PF08389_consen 79 NSPDILEILSQILSQSSSEANEELVKAALKCLKSWISWIPIELIIN--SNLLNLIFQLLQSPE 139 (148)
T ss_dssp HHHHHHHHHHHHHHHHCHCCHHHHHHHHHHHHHHHTTTS-HHHHHS--SSHHHHHHHHTTSCC
T ss_pred HHHHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHhCCHHHhcc--HHHHHHHHHHcCCHH
Confidence 35667777777777766 4567889999999999999876332 235555555555554
No 80
>KOG0211|consensus
Probab=34.67 E-value=3.3e+02 Score=27.62 Aligned_cols=83 Identities=16% Similarity=0.197 Sum_probs=59.3
Q ss_pred CcHHHHHHHHHHHHhhhcccCcchhhHhhhhchHHHHH-----HHHHHhhhhhhhhhHHHHHHHHHHHhhCHHHHHHHhh
Q psy10447 70 PDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFKN-----FWNHRMALDRRNYRQLVDTTVEIANKVGASEIINRVV 144 (166)
Q Consensus 70 PDeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~-----FW~rR~AlDr~~~~~vv~TTv~lA~Kvg~~~il~~iv 144 (166)
-.-+.++.+.+.+...+.+-| +++-+++++|.|+.. ||+|++-+|.=. +||.=+|.....+.++
T Consensus 530 ~v~~Ir~~aa~~l~~l~~~~G--~~w~~~~~i~k~L~~~~q~~y~~R~t~l~si~---------~la~v~g~ei~~~~Ll 598 (759)
T KOG0211|consen 530 HVYSIREAAARNLPALVETFG--SEWARLEEIPKLLAMDLQDNYLVRMTTLFSIH---------ELAEVLGQEITCEDLL 598 (759)
T ss_pred hHHHHHHHHHHHhHHHHHHhC--cchhHHHhhHHHHHHhcCcccchhhHHHHHHH---------HHHHHhccHHHHHHHh
Confidence 356899999999999999999 666789999998863 889999888743 4555555544444444
Q ss_pred ----cccccchHHHHHHHHHHHh
Q psy10447 145 ----DDLKDENEQYRKMVMESIE 163 (166)
Q Consensus 145 ----~~lKDesE~~R~M~~eti~ 163 (166)
+..+|..+.-|-=|.....
T Consensus 599 p~~~~l~~D~vanVR~nvak~L~ 621 (759)
T KOG0211|consen 599 PVFLDLVKDPVANVRINVAKHLP 621 (759)
T ss_pred HHHHHhccCCchhhhhhHHHHHH
Confidence 4556777666655554443
No 81
>PF11113 Phage_head_chap: Head assembly gene product; InterPro: IPR021049 This head assembly protein is also refereed to as gene product 40 (Gp40). A specific gp20-gp40 membrane insertion structure constitutes the T4 prohead assembly initiation complex [].
Probab=34.32 E-value=24 Score=24.77 Aligned_cols=25 Identities=28% Similarity=0.534 Sum_probs=20.6
Q ss_pred HHhhcCCCcHHHHHHHHHHHHhhhc
Q psy10447 63 LIREFQSPDEEMKKIVLKVVKQCCA 87 (166)
Q Consensus 63 l~rEF~SPDeEMKkiVLkVv~qc~~ 87 (166)
|.=+|++|+||-|-.+-.-|.+|..
T Consensus 29 l~vdfsT~~e~~k~el~phVe~ci~ 53 (56)
T PF11113_consen 29 LKVDFSTPSEDRKEELAPHVEKCIQ 53 (56)
T ss_pred EEEEEeCCCcchhhHHHHHHHHHHh
Confidence 3447999999998888888888864
No 82
>KOG3260|consensus
Probab=34.25 E-value=36 Score=29.47 Aligned_cols=27 Identities=19% Similarity=0.441 Sum_probs=23.7
Q ss_pred HHHHHHHHHhhcCCCcHHHHHHHHHHH
Q psy10447 56 TKEVMLILIREFQSPDEEMKKIVLKVV 82 (166)
Q Consensus 56 t~evm~il~rEF~SPDeEMKkiVLkVv 82 (166)
..-+|.++.+=++.-|++||++|-|--
T Consensus 183 ~~glmnvmKk~YeDGD~~mK~tIaKAW 209 (224)
T KOG3260|consen 183 SEGLMNVMKKIYEDGDDDMKQTIAKAW 209 (224)
T ss_pred HHHHHHHHHHHHhcccHHHHHHHHHHH
Confidence 456999999999999999999998753
No 83
>PF08158 NUC130_3NT: NUC130/3NT domain; InterPro: IPR012977 This N-terminal domain is found in a novel nucleolar protein family defined by NUC130/133 [].
Probab=32.73 E-value=1.2e+02 Score=20.49 Aligned_cols=35 Identities=11% Similarity=0.242 Sum_probs=30.3
Q ss_pred hhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHH
Q psy10447 49 AEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVK 83 (166)
Q Consensus 49 ~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~ 83 (166)
|+...-|-.+++.+|...-..=|.|+|+.+.+-+-
T Consensus 10 p~~~~~Fp~~L~~lL~~~~~~L~p~lR~~lv~aLi 44 (52)
T PF08158_consen 10 PKETKDFPQELIDLLRNHHTVLDPDLRMKLVKALI 44 (52)
T ss_pred HHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHH
Confidence 56777889999999999999999999998877654
No 84
>KOG2171|consensus
Probab=32.45 E-value=3.1e+02 Score=29.13 Aligned_cols=103 Identities=17% Similarity=0.229 Sum_probs=61.9
Q ss_pred hHHHHHHHHHhh-cCCCcHHHHHHHHHHHHhhhcc--cCcch---hhHhhhhchHHHHHHHHHHhhhhhhhhhHHHHHHH
Q psy10447 55 YTKEVMLILIRE-FQSPDEEMKKIVLKVVKQCCAT--DGVEA---QYIKDEILPPFFKNFWNHRMALDRRNYRQLVDTTV 128 (166)
Q Consensus 55 Yt~evm~il~rE-F~SPDeEMKkiVLkVv~qc~~t--~gv~~---~yir~~i~~~FF~~FW~rR~AlDr~~~~~vv~TTv 128 (166)
++.-+.+-|..- -+|+|++-|.-..-..++.+.+ .++++ +-||..++.-|++- + .....+.+-++.-
T Consensus 33 ~~~~~l~~L~~i~~~~~~p~~Rq~aaVl~Rkl~~~~w~~l~~e~~~siks~lL~~~~~E----~---~~~vr~k~~dviA 105 (1075)
T KOG2171|consen 33 KTEPLLPALAHILATSADPQVRQLAAVLLRKLLTKHWSRLSAEVQQSIKSSLLEIIQSE----T---EPSVRHKLADVIA 105 (1075)
T ss_pred cccchHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHhc----c---chHHHHHHHHHHH
Confidence 333344433332 2466777766665555555543 12222 22333444333321 1 1224456667788
Q ss_pred HHHHhhCHH---HHHHHhhcccccchHHHHHHHHHHHhh
Q psy10447 129 EIANKVGAS---EIINRVVDDLKDENEQYRKMVMESIEK 164 (166)
Q Consensus 129 ~lA~Kvg~~---~il~~iv~~lKDesE~~R~M~~eti~k 164 (166)
+||++.+-. ++++-|.+-++++++++|.|++..+..
T Consensus 106 eia~~~l~e~WPell~~L~q~~~S~~~~~rE~al~il~s 144 (1075)
T KOG2171|consen 106 EIARNDLPEKWPELLQFLFQSTKSPNPSLRESALLILSS 144 (1075)
T ss_pred HHHHhccccchHHHHHHHHHHhcCCCcchhHHHHHHHHh
Confidence 888887654 999999999999999999999877653
No 85
>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=31.79 E-value=1.3e+02 Score=22.61 Aligned_cols=62 Identities=18% Similarity=0.372 Sum_probs=41.6
Q ss_pred hhhchHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHhh-CHHHHHHHhhcccccchH-HHHHHHHHHHh
Q psy10447 98 DEILPPFFKNFWNHRMALDRRNYRQLVDTTVEIANKV-GASEIINRVVDDLKDENE-QYRKMVMESIE 163 (166)
Q Consensus 98 ~~i~~~FF~~FW~rR~AlDr~~~~~vv~TTv~lA~Kv-g~~~il~~iv~~lKDesE-~~R~M~~eti~ 163 (166)
+.++.++.+-+|.. |....+.++++.++-|..- .......+++..+..... .||...++.+.
T Consensus 17 ~~~~~~l~~~~~~~----~~~~~~~i~~~i~~~a~~~~~~~~~~a~l~~~l~~~~~~~f~~~ll~~~~ 80 (209)
T PF02854_consen 17 ESIIDELIKLNWSD----DPETLKEIVKLIFEKAVEEPNFSPLYARLCAALNSRFPSEFRSLLLNRCQ 80 (209)
T ss_dssp HHHHHHHHHHHHHS----CHHHHHHHHHHHHHHHHHSGGGHHHHHHHHHHHHHHCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhc----cHHHHHHHHHHHhhhhhcCchHHHHHHHHHHHHhccchhhHHHHHHHHHH
Confidence 56677777777766 5556666666666655544 566667777777766666 78877777654
No 86
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=31.47 E-value=93 Score=20.38 Aligned_cols=32 Identities=22% Similarity=0.257 Sum_probs=23.2
Q ss_pred HHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhc
Q psy10447 56 TKEVMLILIREFQSPDEEMKKIVLKVVKQCCA 87 (166)
Q Consensus 56 t~evm~il~rEF~SPDeEMKkiVLkVv~qc~~ 87 (166)
..|+...|..+|.-|.++.++-|...+.++..
T Consensus 32 ~~ei~~~l~~~y~~~~~~~~~dv~~fl~~L~~ 63 (68)
T PF05402_consen 32 VEEIVDALAEEYDVDPEEAEEDVEEFLEQLRE 63 (68)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHH
Confidence 35677778888888888888888888887764
No 87
>PF08389 Xpo1: Exportin 1-like protein; InterPro: IPR013598 The exchange of macromolecules between the nucleus and cytoplasm takes place through nuclear pore complexes within the nuclear membrane. Active transport of large molecules through these pore complexes require carrier proteins, called karyopherins (importins and exportins), which shuttle between the two compartments. This domain is found close to the N terminus of yeast exportin 1 (Xpo1, Crm1, P14068 from SWISSPROT), as well as adjacent to the N-terminal domain of importin-beta (IPR001494 from INTERPRO). Exportin 1 is a nuclear export receptor that translocates proteins out of the nucleus; it interacts with leucine-rich nuclear export signal (NES) sequences in proteins to be transported, as well as with RanGTP [, ]. Importin-beta is a nuclear import receptor that translocates proteins into the nucleus; it interacts with RanGTP and importin-alpha, the latter binding with the nuclear localisation signal (NLS) sequences in proteins to be transported []. More information about these proteins can be found at Protein of the Month: Importins [].; PDB: 3IBV_A 3ICQ_U 3M1I_C 3NC1_A 3NBY_D 3NBZ_D 3NC0_A 3GJX_D 2XWU_B 2X19_B ....
Probab=31.04 E-value=1.1e+02 Score=22.02 Aligned_cols=43 Identities=23% Similarity=0.318 Sum_probs=26.5
Q ss_pred HHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhHhh-hhchHHHHH
Q psy10447 63 LIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIKD-EILPPFFKN 107 (166)
Q Consensus 63 l~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~-~i~~~FF~~ 107 (166)
+....+..+++|.+.+|++++.++. -+.+.++-+ .+++-.|+.
T Consensus 91 l~~~~~~~~~~~~~~~L~~l~s~i~--~~~~~~i~~~~~l~~~~~~ 134 (148)
T PF08389_consen 91 LSQSSSEANEELVKAALKCLKSWIS--WIPIELIINSNLLNLIFQL 134 (148)
T ss_dssp HHHHCHCCHHHHHHHHHHHHHHHTT--TS-HHHHHSSSHHHHHHHH
T ss_pred HHhhccccHHHHHHHHHHHHHHHHH--hCCHHHhccHHHHHHHHHH
Confidence 3333333448889999999998887 555555533 355555543
No 88
>cd07064 AlkD_like_1 A new structural DNA glycosylase containing HEAT-like repeats. This domain represents a new and uncharacterized structural superfamily of DNA glycosylases that form an alpha-alpha superhelix fold that are not belong to the identified five structural DNA glycosylase superfamilies (UDG, AAG/MNPG, MutM/Fpg and helix-hairpin-helix). DNA glycosylases removing alkylated base residues have been identified in all organisms investigated and may be universally present in nature. DNA glycosylases catalyze the first step in Base Excision Repair (BER) pathway by cleaving damaged DNA bases within double strand DNA to produce an abasic site. The resulting abasic site is further processed by AP endonuclease, phosphodiesterase, DNA polymerases, and DNA ligase functions to restore the DNA to an undamaged state. All glycosylase examined to date utilize a similar strategy for binding DNA and base flipping despite their structural diversity. The known structures for members of this fa
Probab=31.04 E-value=3e+02 Score=22.57 Aligned_cols=43 Identities=16% Similarity=0.329 Sum_probs=26.8
Q ss_pred HHHHHHhhhhhhhhhHHHHHHHHHHHhhCHHHHHHHhhcccccchHHHHHHHH
Q psy10447 107 NFWNHRMALDRRNYRQLVDTTVEIANKVGASEIINRVVDDLKDENEQYRKMVM 159 (166)
Q Consensus 107 ~FW~rR~AlDr~~~~~vv~TTv~lA~Kvg~~~il~~iv~~lKDesE~~R~M~~ 159 (166)
++|.||.|.- +++...++.+...+.+ ++..+-++.|-|=++++
T Consensus 128 ~~W~rR~ai~---------~~l~~~~~~~~~~l~~-~~~~~~~d~e~fI~KAi 170 (208)
T cd07064 128 NFWLRRTAIL---------HQLKYKEKTDTDLLFE-IILANLGSKEFFIRKAI 170 (208)
T ss_pred cHHHHHHHHH---------HHHHHHHccCHHHHHH-HHHHhCCChHHHHHHHH
Confidence 4899999985 3555677766555554 44444445566655554
No 89
>PF06743 FAST_1: FAST kinase-like protein, subdomain 1; InterPro: IPR010622 This entry represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis []. Note that many family members are hypothetical proteins.; GO: 0004672 protein kinase activity
Probab=30.94 E-value=1.8e+02 Score=20.02 Aligned_cols=68 Identities=16% Similarity=0.220 Sum_probs=49.7
Q ss_pred HHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhHhhhhchHHHH
Q psy10447 34 AAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFK 106 (166)
Q Consensus 34 AaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~ 106 (166)
++.|.+.|.+= -+|.-+...-+-+...|.+.|..-+.++ .|.++=.||.-+-...++|..-.=|.|.+
T Consensus 2 ~~il~~fa~LN--y~P~~~~~f~~~~~~~L~~~l~~~~p~~---ll~~v~Sl~~l~~~p~~~l~~vf~~~Fl~ 69 (71)
T PF06743_consen 2 ASILLPFARLN--YQPPNAEEFFEKLIERLESYLDEFSPED---LLDLVWSLCLLQRFPEDLLNKVFSPDFLQ 69 (71)
T ss_pred HHHHHHHHhcC--CCCCCHHHHHHHHHHHHHHhcccCCHHH---HHHHHHHHHHHhhCCHHHHHHHcCHHHHh
Confidence 56667777663 3566666666667777888888777554 89999999999999999986555555543
No 90
>PHA00148 lower collar protein
Probab=30.70 E-value=36 Score=30.00 Aligned_cols=25 Identities=24% Similarity=0.674 Sum_probs=20.6
Q ss_pred chhhHhhhhchHHHHHHHHHHhhhhh
Q psy10447 92 EAQYIKDEILPPFFKNFWNHRMALDR 117 (166)
Q Consensus 92 ~~~yir~~i~~~FF~~FW~rR~AlDr 117 (166)
...| |+++=..|-++||+|+++..-
T Consensus 44 Desy-rkefe~~Fik~Fy~rEIGfeT 68 (242)
T PHA00148 44 DESY-RKEFETHFIKHFYNREIGFET 68 (242)
T ss_pred hHHH-HHHHHHHHHHHHHHHHhcCcc
Confidence 3445 888889999999999998753
No 91
>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=30.54 E-value=28 Score=26.03 Aligned_cols=47 Identities=23% Similarity=0.400 Sum_probs=37.8
Q ss_pred CCccccCCcchhhhhhhhHHHHHHHHhhhcchHHHHHHHHhhhcccC
Q psy10447 1 MTDIHCHTLSIESFDSVLKPLWKGIRTHRGKGLAAFLKAIGYLIPLM 47 (166)
Q Consensus 1 ~~~~as~PYGIEsFd~VL~plW~Gir~hRGK~LAaFLKaiG~IIPLM 47 (166)
|.+||..-|--+.+..|++-||+-+....||.----+||+--|==|+
T Consensus 24 l~eIa~~t~~~~~~~~I~~~l~kRL~~~~~k~wr~~~KaL~ll~yLl 70 (125)
T PF01417_consen 24 LAEIAQLTYNSKDCQEIMDVLWKRLSKSDGKNWRHVYKALTLLEYLL 70 (125)
T ss_dssp HHHHHHHTTSCHHHHHHHHHHHHHHHSSTSSGHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhccccHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHHHH
Confidence 34667777777899999999999997788888888888887764444
No 92
>PF13212 DUF4020: Domain of unknown function (DUF4020)
Probab=30.47 E-value=1.9e+02 Score=24.46 Aligned_cols=57 Identities=19% Similarity=0.320 Sum_probs=40.6
Q ss_pred hhcchHHHHHHH---Hhhh-cccCChhHHhh---------hHHHHHHHHHhhcCCCcHHHHHHHHHHHHhh
Q psy10447 28 HRGKGLAAFLKA---IGYL-IPLMDAEYANY---------YTKEVMLILIREFQSPDEEMKKIVLKVVKQC 85 (166)
Q Consensus 28 hRGK~LAaFLKa---iG~I-IPLMD~eyA~y---------Yt~evm~il~rEF~SPDeEMKkiVLkVv~qc 85 (166)
--++-|+.|++= +|.| ++|=+.||.-- +..+...++++.+ +|+.||+-..++.+.|-
T Consensus 56 ~W~~WL~~fl~~r~R~~gIp~~lt~~E~~~ml~~ll~l~evf~~~le~Iv~~~-~~~~E~~~l~~~~L~k~ 125 (180)
T PF13212_consen 56 FWDAWLSQFLRNRPRMGGIPVSLTPREYVMMLRWLLELPEVFESGLEIIVSGP-CNQLEMKQLFWRILEKK 125 (180)
T ss_pred HHHHHHHHHHhcCccccCCCcCCCcHHHHHHHHHHHhChHHHHHHHHHHHhCC-CcchhHHHHHHHHHHHH
Confidence 345778888865 5555 66767777532 3445556667777 99999999999988873
No 93
>TIGR03495 phage_LysB phage lysis regulatory protein, LysB family. Members of this protein family are phage lysis regulatory protein, including the well-studied protein LysB (lysis protein B) of Enterobacteria phage P2. For members of this family, genes are found in phage or in prophage regions of bacterial genomes, typically near a phage lysozyme or phage holin.
Probab=30.40 E-value=20 Score=28.68 Aligned_cols=19 Identities=32% Similarity=0.506 Sum_probs=15.4
Q ss_pred HHHhhcccccchHHHHHHH
Q psy10447 140 INRVVDDLKDENEQYRKMV 158 (166)
Q Consensus 140 l~~iv~~lKDesE~~R~M~ 158 (166)
-++-+..||||||.||+=+
T Consensus 80 re~~i~rL~~ENe~lR~Wa 98 (135)
T TIGR03495 80 REQRIERLKRENEDLRRWA 98 (135)
T ss_pred HHHHHHHHHHcCHHHHHHh
Confidence 4567788999999999854
No 94
>cd05498 Bromo_Brdt_II_like Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=30.31 E-value=1.4e+02 Score=21.48 Aligned_cols=82 Identities=17% Similarity=0.288 Sum_probs=48.6
Q ss_pred HHHHHHhhhcchHHHHHHHHhhhcccCCh---hHHhhhHH--------HHHH-HHHhhcCCCcHHHHHHHHHHHHhhhcc
Q psy10447 21 LWKGIRTHRGKGLAAFLKAIGYLIPLMDA---EYANYYTK--------EVML-ILIREFQSPDEEMKKIVLKVVKQCCAT 88 (166)
Q Consensus 21 lW~Gir~hRGK~LAaFLKaiG~IIPLMD~---eyA~yYt~--------evm~-il~rEF~SPDeEMKkiVLkVv~qc~~t 88 (166)
+.+-+.+|+|+-+|. -|+-|+ || ++.+||.. .|-. +-.+++.|+ +|...-+..+..+|-.-
T Consensus 8 il~~l~~~~~~~~a~-----~F~~pv-~~~~~~~p~Y~~~I~~Pmdl~~I~~kl~~~~Y~s~-~ef~~D~~li~~Na~~y 80 (102)
T cd05498 8 ILKELFSKKHKAYAW-----PFYKPV-DPEALGLHDYHDIIKHPMDLSTIKKKLDNREYADA-QEFAADVRLMFSNCYKY 80 (102)
T ss_pred HHHHHHhCCCccccC-----cccCcC-CccccCCCcHHHHccCCCcHHHHHHHHccCCCCCH-HHHHHHHHHHHHHHHHH
Confidence 556677777766543 122232 43 36788853 1111 223467776 78888899999999877
Q ss_pred cCcchhhH-hhhhchHHHHHHH
Q psy10447 89 DGVEAQYI-KDEILPPFFKNFW 109 (166)
Q Consensus 89 ~gv~~~yi-r~~i~~~FF~~FW 109 (166)
-|-..... --..+..+|+.=|
T Consensus 81 n~~~s~i~~~a~~l~~~fe~~~ 102 (102)
T cd05498 81 NPPDHPVHAMARKLQDVFEDRW 102 (102)
T ss_pred CCCCCHHHHHHHHHHHHHHHhC
Confidence 66654432 3455566666554
No 95
>COG1413 FOG: HEAT repeat [Energy production and conversion]
Probab=30.09 E-value=92 Score=26.18 Aligned_cols=32 Identities=19% Similarity=0.367 Sum_probs=19.8
Q ss_pred hCHHHHHHHhhcccccchHHHHHHHHHHHhhc
Q psy10447 134 VGASEIINRVVDDLKDENEQYRKMVMESIEKT 165 (166)
Q Consensus 134 vg~~~il~~iv~~lKDesE~~R~M~~eti~kv 165 (166)
.|..+.+.-+...+.|++...|..++.++.++
T Consensus 70 ~~~~~av~~l~~~l~d~~~~vr~~a~~aLg~~ 101 (335)
T COG1413 70 LGSEEAVPLLRELLSDEDPRVRDAAADALGEL 101 (335)
T ss_pred hchHHHHHHHHHHhcCCCHHHHHHHHHHHHcc
Confidence 56666666666666666666666666655543
No 96
>KOG1020|consensus
Probab=29.50 E-value=7.5e+02 Score=27.70 Aligned_cols=140 Identities=15% Similarity=0.260 Sum_probs=97.7
Q ss_pred hhhhhhhHHHHHHHHhhhcchHHHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCc
Q psy10447 12 ESFDSVLKPLWKGIRTHRGKGLAAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGV 91 (166)
Q Consensus 12 EsFd~VL~plW~Gir~hRGK~LAaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv 91 (166)
-+||+.|.-+-.++.+..-+.=+..|||+..|+-. ||.-- =-.+|-.-+.+-|+..----|-++|-.|-..+.+
T Consensus 812 ~sfD~yLk~Il~~l~e~~ialRtkAlKclS~ive~-Dp~vL--~~~dvq~~Vh~R~~DssasVREAaldLvGrfvl~--- 885 (1692)
T KOG1020|consen 812 QSFDPYLKLILSVLGENAIALRTKALKCLSMIVEA-DPSVL--SRPDVQEAVHGRLNDSSASVREAALDLVGRFVLS--- 885 (1692)
T ss_pred HhhHHHHHHHHHHhcCchHHHHHHHHHHHHHHHhc-ChHhh--cCHHHHHHHHHhhccchhHHHHHHHHHHhhhhhc---
Confidence 47999999999999888777778889999998865 55431 1245666677788888888888888888776664
Q ss_pred chhhHhhhhchHHHHHHHHHH----hhhhhhhhhHHH---HHHHHHHHhhCHHHHHHHhhcccccchHHHHHHHHHHHhh
Q psy10447 92 EAQYIKDEILPPFFKNFWNHR----MALDRRNYRQLV---DTTVEIANKVGASEIINRVVDDLKDENEQYRKMVMESIEK 164 (166)
Q Consensus 92 ~~~yir~~i~~~FF~~FW~rR----~AlDr~~~~~vv---~TTv~lA~Kvg~~~il~~iv~~lKDesE~~R~M~~eti~k 164 (166)
..+.++.||..--.|= ++.=+|--|++- +.|-.+.. ..+|..+++--.-||.+...+||-|+..|
T Consensus 886 -----~~e~~~qyY~~i~erIlDtgvsVRKRvIKIlrdic~e~pdf~~---i~~~cakmlrRv~DEEg~I~kLv~etf~k 957 (1692)
T KOG1020|consen 886 -----IPELIFQYYDQIIERILDTGVSVRKRVIKILRDICEETPDFSK---IVDMCAKMLRRVNDEEGNIKKLVRETFLK 957 (1692)
T ss_pred -----cHHHHHHHHHHHHhhcCCCchhHHHHHHHHHHHHHHhCCChhh---HHHHHHHHHHHhccchhHHHHHHHHHHHH
Confidence 3455667777654432 122233333333 33333433 45677788888899999999999999876
Q ss_pred c
Q psy10447 165 T 165 (166)
Q Consensus 165 v 165 (166)
.
T Consensus 958 l 958 (1692)
T KOG1020|consen 958 L 958 (1692)
T ss_pred H
Confidence 3
No 97
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=29.44 E-value=1.7e+02 Score=19.60 Aligned_cols=46 Identities=22% Similarity=0.392 Sum_probs=31.0
Q ss_pred HHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhHhhhhchHHHH
Q psy10447 56 TKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFK 106 (166)
Q Consensus 56 t~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~ 106 (166)
..+.+.-...+|+-|.| .|+..++.|......+..|+ +.|+....+
T Consensus 17 e~~~i~~~~~~~~~~~e----vI~~ai~~a~~~~~~~~~Yi-~~Il~~W~~ 62 (73)
T TIGR01446 17 EMEDLKYWLDEFGNSPE----LIKEALKEAVSNNKANYKYI-DAILNNWKN 62 (73)
T ss_pred HHHHHHHHHHHhCCCHH----HHHHHHHHHHHcCCCCHHHH-HHHHHHHHH
Confidence 34445556677776644 67788888887666778897 567665543
No 98
>KOG2137|consensus
Probab=29.32 E-value=1.9e+02 Score=29.11 Aligned_cols=26 Identities=27% Similarity=0.452 Sum_probs=14.6
Q ss_pred CCcHHHHHHHHHHHHhhhcccCcchh
Q psy10447 69 SPDEEMKKIVLKVVKQCCATDGVEAQ 94 (166)
Q Consensus 69 SPDeEMKkiVLkVv~qc~~t~gv~~~ 94 (166)
+|+||.|-.||.++.-|..+.-+..+
T Consensus 381 t~~e~~~~~IlplL~~S~~~~~~~iQ 406 (700)
T KOG2137|consen 381 TPPEEVKEKILPLLYRSLEDSDVQIQ 406 (700)
T ss_pred CChHHHHHHHHHHHHHHhcCcchhhH
Confidence 45556666666666655555544443
No 99
>PF05536 Neurochondrin: Neurochondrin
Probab=28.66 E-value=1.7e+02 Score=27.81 Aligned_cols=86 Identities=14% Similarity=0.087 Sum_probs=66.9
Q ss_pred cccCCcchhhhhh--hhHHHHHHHHhhhcchHHHHHHHHhhhcccCChhHHhhhHHH---HHHHHHhhcCCCcHHHHHHH
Q psy10447 4 IHCHTLSIESFDS--VLKPLWKGIRTHRGKGLAAFLKAIGYLIPLMDAEYANYYTKE---VMLILIREFQSPDEEMKKIV 78 (166)
Q Consensus 4 ~as~PYGIEsFd~--VL~plW~Gir~hRGK~LAaFLKaiG~IIPLMD~eyA~yYt~e---vm~il~rEF~SPDeEMKkiV 78 (166)
++++|=|-++|=. .+.+|-.-+.+ .+......++.+..+.--.+.+..+.+.++ +..-|.++|++...+-|=.+
T Consensus 126 Ias~~~G~~aLl~~g~v~~L~ei~~~-~~~~~E~Al~lL~~Lls~~~~~~~~~~~~~l~~il~~La~~fs~~~~~~kfel 204 (543)
T PF05536_consen 126 IASSPEGAKALLESGAVPALCEIIPN-QSFQMEIALNLLLNLLSRLGQKSWAEDSQLLHSILPSLARDFSSFHGEDKFEL 204 (543)
T ss_pred HHcCcHhHHHHHhcCCHHHHHHHHHh-CcchHHHHHHHHHHHHHhcchhhhhhhHHHHHHHHHHHHHHHHhhccchHHHH
Confidence 6788889888876 77788877777 777778888888888766666555555554 44559999999999999999
Q ss_pred HHHHHhhhcccC
Q psy10447 79 LKVVKQCCATDG 90 (166)
Q Consensus 79 LkVv~qc~~t~g 90 (166)
|.++........
T Consensus 205 l~~L~~~L~~~~ 216 (543)
T PF05536_consen 205 LEFLSAFLPRSP 216 (543)
T ss_pred HHHHHHhcCcCC
Confidence 999888777764
No 100
>KOG0166|consensus
Probab=28.64 E-value=4.3e+02 Score=25.70 Aligned_cols=142 Identities=18% Similarity=0.261 Sum_probs=84.7
Q ss_pred hHHHHHHHHhhhcchHHHHHHHHhhhcc--------------------cCChhHHhh-----------------------
Q psy10447 18 LKPLWKGIRTHRGKGLAAFLKAIGYLIP--------------------LMDAEYANY----------------------- 54 (166)
Q Consensus 18 L~plW~Gir~hRGK~LAaFLKaiG~IIP--------------------LMD~eyA~y----------------------- 54 (166)
+.-|=+.+.+.-++...+-|+|+|+|+- ||...|...
T Consensus 281 v~~LV~lL~~~~~~v~~PaLRaiGNIvtG~d~QTq~vi~~~~L~~l~~ll~~s~~~~ikkEAcW~iSNItAG~~~qiqaV 360 (514)
T KOG0166|consen 281 VPRLVDLLGHSSPKVVTPALRAIGNIVTGSDEQTQVVINSGALPVLSNLLSSSPKESIKKEACWTISNITAGNQEQIQAV 360 (514)
T ss_pred hHHHHHHHcCCCcccccHHHhhccceeeccHHHHHHHHhcChHHHHHHHhccCcchhHHHHHHHHHHHhhcCCHHHHHHH
Confidence 3344556667778888899999999542 222111111
Q ss_pred hHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcch-hhH-hhhhchHHHHHHHHHHhhhhhhhhhHHHHHHHHHHH
Q psy10447 55 YTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEA-QYI-KDEILPPFFKNFWNHRMALDRRNYRQLVDTTVEIAN 132 (166)
Q Consensus 55 Yt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~-~yi-r~~i~~~FF~~FW~rR~AlDr~~~~~vv~TTv~lA~ 132 (166)
-...+++.|++=.++-|-++||-..-+|.+|+++.-... .|+ ..-+++||=.-+ +..|.+....+.++ .+.-.
T Consensus 361 ida~l~p~Li~~l~~~ef~~rKEAawaIsN~ts~g~~~qi~yLv~~giI~plcdlL----~~~D~~ii~v~Ld~-l~nil 435 (514)
T KOG0166|consen 361 IDANLIPVLINLLQTAEFDIRKEAAWAISNLTSSGTPEQIKYLVEQGIIKPLCDLL----TCPDVKIILVALDG-LENIL 435 (514)
T ss_pred HHcccHHHHHHHHhccchHHHHHHHHHHHhhcccCCHHHHHHHHHcCCchhhhhcc----cCCChHHHHHHHHH-HHHHH
Confidence 122478888999999999999999999999887765322 232 455666665544 66777763333333 22322
Q ss_pred hhCHH----------------HHHHHhhcccccchHHHHHHHHHHHhh
Q psy10447 133 KVGAS----------------EIINRVVDDLKDENEQYRKMVMESIEK 164 (166)
Q Consensus 133 Kvg~~----------------~il~~iv~~lKDesE~~R~M~~eti~k 164 (166)
|+|-. +-++.|=.-=-.|||...+.+..-|++
T Consensus 436 ~~~e~~~~~~~n~~~~~IEe~ggldkiE~LQ~hen~~Iy~~A~~II~~ 483 (514)
T KOG0166|consen 436 KVGEAEKNRGTNPLAIMIEEAGGLDKIENLQSHENEEIYKKAYKIIDT 483 (514)
T ss_pred HHHHHhccccccHHHHHHHHccChhHHHHhhccccHHHHHHHHHHHHH
Confidence 33222 122233333345777787777766654
No 101
>PRK09623 vorD 2-ketoisovalerate ferredoxin oxidoreductase subunit delta; Reviewed
Probab=28.58 E-value=12 Score=27.61 Aligned_cols=23 Identities=43% Similarity=0.501 Sum_probs=19.2
Q ss_pred cCCCcHHHHHHHHHHHHhhhccc
Q psy10447 67 FQSPDEEMKKIVLKVVKQCCATD 89 (166)
Q Consensus 67 F~SPDeEMKkiVLkVv~qc~~t~ 89 (166)
|..-.||-||++||++++++...
T Consensus 5 ~~~~~~~~~~~~~~~~~~~p~~~ 27 (105)
T PRK09623 5 FGEKKEEAKKIVLKSVDEYPEAP 27 (105)
T ss_pred hhcccccccccCchhhhcCCCcc
Confidence 55667899999999999988654
No 102
>PF07571 DUF1546: Protein of unknown function (DUF1546); InterPro: IPR011442 These proteins are associated with IPR004823 from INTERPRO in transcription initiation factor TFIID subunit 6 (TAF6).; GO: 0051090 regulation of sequence-specific DNA binding transcription factor activity, 0005634 nucleus
Probab=28.55 E-value=1.6e+02 Score=21.41 Aligned_cols=36 Identities=8% Similarity=0.206 Sum_probs=29.4
Q ss_pred HhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhc
Q psy10447 52 ANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCA 87 (166)
Q Consensus 52 A~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~ 87 (166)
--.|...++..|.+.|+++...+|--|.+.+.+...
T Consensus 22 LRd~AA~lL~~I~~~~~~~~~~L~~Ri~~tl~k~l~ 57 (92)
T PF07571_consen 22 LRDFAASLLAQICRKFSSSYPTLQPRITRTLLKALL 57 (92)
T ss_pred HHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHc
Confidence 567888999999999999999999877777665544
No 103
>PF10266 Strumpellin: Hereditary spastic paraplegia protein strumpellin; InterPro: IPR019393 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53. Strumpellin contains one known domain called a spectrin repeat that consists of three alpha-helices of a characteristic length wrapped in a left-handed coiled coil. The spectrin proteins have multiple copies of this repeat, which can then form multimers in the cell. Spectrin associates with the cell membrane via spectrin repeats in the ankyrin protein. The spectrin repeat is a structural platform for cytoskeletal protein assemblies. Two closely situated point mutations in human strumpellin lead to the condition of hereditary spastic paraplegia.
Probab=27.91 E-value=4.5e+02 Score=27.87 Aligned_cols=80 Identities=25% Similarity=0.380 Sum_probs=62.4
Q ss_pred cccCCcchhhhhhhhHHHHHHHHhhhcchH---HHHHHHHhhh-cccC--------Ch-hHHhhhHHHHHHHHHhhcCCC
Q psy10447 4 IHCHTLSIESFDSVLKPLWKGIRTHRGKGL---AAFLKAIGYL-IPLM--------DA-EYANYYTKEVMLILIREFQSP 70 (166)
Q Consensus 4 ~as~PYGIEsFd~VL~plW~Gir~hRGK~L---AaFLKaiG~I-IPLM--------D~-eyA~yYt~evm~il~rEF~SP 70 (166)
++-.-||.+.-++-.+-+.++|++.=.-++ |-|||--..+ +||+ |- .-++||..|+..-+.+=.+.=
T Consensus 526 i~D~SYaW~li~~~~~~mQ~~Ik~~P~~v~~lRa~FlKLaS~L~~pl~Ri~Q~~s~Dl~sVS~yYS~eLv~~vR~VLqiI 605 (1081)
T PF10266_consen 526 ISDFSYAWELIDSYTPIMQQRIKKDPSTVIKLRATFLKLASALELPLLRINQAESPDLSSVSQYYSSELVKYVRKVLQII 605 (1081)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHhccHHHHhcccccchHHHHHHHHHHHHHHHHHHHHHHh
Confidence 344568999999999999999999887766 9999965544 7988 22 449999999999888877776
Q ss_pred cHHHHHHHHHHHH
Q psy10447 71 DEEMKKIVLKVVK 83 (166)
Q Consensus 71 DeEMKkiVLkVv~ 83 (166)
-+-|=.++-+|+.
T Consensus 606 P~smF~il~~ii~ 618 (1081)
T PF10266_consen 606 PESMFEILAQIID 618 (1081)
T ss_pred HHHHHHHHHHHHH
Confidence 6666666666663
No 104
>PLN03200 cellulose synthase-interactive protein; Provisional
Probab=27.82 E-value=6.6e+02 Score=28.67 Aligned_cols=143 Identities=8% Similarity=0.063 Sum_probs=85.9
Q ss_pred hhHHHHHHHHhhhcchHHHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhH
Q psy10447 17 VLKPLWKGIRTHRGKGLAAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYI 96 (166)
Q Consensus 17 VL~plW~Gir~hRGK~LAaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yi 96 (166)
.+.+|++-++......--.=+.++|.|----|..-..-=.....+.|++=.+|||++.|+--.-++-+++..+.=....+
T Consensus 447 gIp~LV~LL~s~s~~iQ~~A~~~L~nLa~~ndenr~aIieaGaIP~LV~LL~s~~~~iqeeAawAL~NLa~~~~qir~iV 526 (2102)
T PLN03200 447 GVQLLISLLGLSSEQQQEYAVALLAILTDEVDESKWAITAAGGIPPLVQLLETGSQKAKEDSATVLWNLCCHSEDIRACV 526 (2102)
T ss_pred cHHHHHHHHcCCCHHHHHHHHHHHHHHHcCCHHHHHHHHHCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhCCcHHHHHHH
Confidence 35566666655443333333455555522111111122223467788888999999999999999999887432222333
Q ss_pred -hhhhchHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHhhCHHHHHHHhhcccccchHHHHHHHHHHHhh
Q psy10447 97 -KDEILPPFFKNFWNHRMALDRRNYRQLVDTTVEIANKVGASEIINRVVDDLKDENEQYRKMVMESIEK 164 (166)
Q Consensus 97 -r~~i~~~FF~~FW~rR~AlDr~~~~~vv~TTv~lA~Kvg~~~il~~iv~~lKDesE~~R~M~~eti~k 164 (166)
+...+|++.+-. +. -|.+..+....|-..|++ .|-.+++..++.-|..++......+++++..
T Consensus 527 ~~aGAIppLV~LL---~s-gd~~~q~~Aa~AL~nLi~-~~d~~~I~~Lv~LLlsdd~~~~~~aL~vLgn 590 (2102)
T PLN03200 527 ESAGAVPALLWLL---KN-GGPKGQEIAAKTLTKLVR-TADAATISQLTALLLGDLPESKVHVLDVLGH 590 (2102)
T ss_pred HHCCCHHHHHHHH---hC-CCHHHHHHHHHHHHHHHh-ccchhHHHHHHHHhcCCChhHHHHHHHHHHH
Confidence 346787765542 11 244444455566566655 4666778888888888888888888877643
No 105
>PF04826 Arm_2: Armadillo-like; InterPro: IPR006911 This entry consists of mammalian proteins of unknown function.
Probab=27.39 E-value=1.5e+02 Score=25.41 Aligned_cols=69 Identities=20% Similarity=0.316 Sum_probs=48.5
Q ss_pred HHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhHhhhhchHHHH
Q psy10447 35 AFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFK 106 (166)
Q Consensus 35 aFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~ 106 (166)
+=||+++++ .+-| +|-.-- ...++-+.+=.++-++..|--+||++-+.......+.+.+..+.++.|..
T Consensus 114 agLrlL~nL-tv~~-~~~~~l-~~~i~~ll~LL~~G~~~~k~~vLk~L~nLS~np~~~~~Ll~~q~~~~~~~ 182 (254)
T PF04826_consen 114 AGLRLLTNL-TVTN-DYHHML-ANYIPDLLSLLSSGSEKTKVQVLKVLVNLSENPDMTRELLSAQVLSSFLS 182 (254)
T ss_pred HHHHHHHcc-CCCc-chhhhH-HhhHHHHHHHHHcCChHHHHHHHHHHHHhccCHHHHHHHHhccchhHHHH
Confidence 346777776 3444 221111 11233445556788999999999999999999999999999998777764
No 106
>COG1413 FOG: HEAT repeat [Energy production and conversion]
Probab=27.21 E-value=3.1e+02 Score=22.99 Aligned_cols=91 Identities=16% Similarity=0.213 Sum_probs=61.0
Q ss_pred HHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhHhhhhchHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHhhCH
Q psy10447 57 KEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFKNFWNHRMALDRRNYRQLVDTTVEIANKVGA 136 (166)
Q Consensus 57 ~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~FW~rR~AlDr~~~~~vv~TTv~lA~Kvg~ 136 (166)
.+....+.+-+.++|..-|.....++.+.-..+.+.+ +++-+-.+= + .+-.+.+.---++|.
T Consensus 42 ~~~~~~~~~~l~~~~~~vr~~aa~~l~~~~~~~av~~--l~~~l~d~~---~-------------~vr~~a~~aLg~~~~ 103 (335)
T COG1413 42 PEAADELLKLLEDEDLLVRLSAAVALGELGSEEAVPL--LRELLSDED---P-------------RVRDAAADALGELGD 103 (335)
T ss_pred hhhHHHHHHHHcCCCHHHHHHHHHHHhhhchHHHHHH--HHHHhcCCC---H-------------HHHHHHHHHHHccCC
Confidence 4667778889999999999888877555444444333 111111110 0 222333333345888
Q ss_pred HHHHHHhhcccc-cchHHHHHHHHHHHhhc
Q psy10447 137 SEIINRVVDDLK-DENEQYRKMVMESIEKT 165 (166)
Q Consensus 137 ~~il~~iv~~lK-DesE~~R~M~~eti~kv 165 (166)
.+-+..++..|+ |+|+.-|.-+..++.++
T Consensus 104 ~~a~~~li~~l~~d~~~~vR~~aa~aL~~~ 133 (335)
T COG1413 104 PEAVPPLVELLENDENEGVRAAAARALGKL 133 (335)
T ss_pred hhHHHHHHHHHHcCCcHhHHHHHHHHHHhc
Confidence 999999999999 89999999999998775
No 107
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=27.18 E-value=95 Score=25.40 Aligned_cols=40 Identities=20% Similarity=0.175 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhhCHHHHHHHhhcccccchHHHHHHHHHHH
Q psy10447 123 LVDTTVEIANKVGASEIINRVVDDLKDENEQYRKMVMESI 162 (166)
Q Consensus 123 vv~TTv~lA~Kvg~~~il~~iv~~lKDesE~~R~M~~eti 162 (166)
...|...||+|+||+.+.-.+|-....|-..=..-.+|++
T Consensus 103 ~~wTr~~LAkkF~~S~~fV~~v~~~~~e~~~~~~~~le~~ 142 (164)
T PF12824_consen 103 EKWTRKKLAKKFNCSPLFVSMVAPAPKEKKKEMEARLEAI 142 (164)
T ss_pred hHhhHHHHHHHhCCCHHHHHHhcCCCHHHHHHHHHHHHHH
Confidence 4678899999999999998888877665444433344433
No 108
>PF05327 RRN3: RNA polymerase I specific transcription initiation factor RRN3; InterPro: IPR007991 This family consists of several eukaryotic proteins which are homologous to the Saccharomyces cerevisiae RRN3 protein. RRN3 is one of the RRN genes specifically required for the transcription of rDNA by RNA polymerase I (Pol I) in the S. cerevisiae [] RNA polymerase I complex within the nucleolus. In mammalian cells, the phosphorylation state of Rrn3 regulates rDNA transcription by determining the steady-state concentration of the Rrn3 [].; PDB: 3TJ1_B.
Probab=27.13 E-value=1.5e+02 Score=28.08 Aligned_cols=71 Identities=23% Similarity=0.402 Sum_probs=50.5
Q ss_pred chHHHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhHhhhhchHHHHHHH
Q psy10447 31 KGLAAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFKNFW 109 (166)
Q Consensus 31 K~LAaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~FW 109 (166)
..|..+|+|++..++++|..+... |-.+|.=..-+-+++..+.-+.-+.+++.+. +.|+ ..++.-..++|=
T Consensus 51 ~~l~~~L~~L~~~Vs~Ld~~~~~L----V~ail~~~W~~~~~~~v~~y~~Fl~~Lvsa~---~~yl-~~vl~~LV~~f~ 121 (563)
T PF05327_consen 51 SQLIRWLKALSSCVSLLDSSCKQL----VEAILSLNWLGRDEDFVEAYIQFLINLVSAQ---PKYL-SPVLSMLVKNFI 121 (563)
T ss_dssp HHHHHHHHHHHHGGGGG-SCCHHH----HHHHHT-TGGGS-HHHHHHHHHHHHHHHHH----GGGH-HHHHHHHHHGGG
T ss_pred HHHHHHHHHHHHHHHHhhhHHHHH----HHHHHcCCCCCCCHHHHHHHHHHHHHHHHhh---HHHH-HHHHHHHHHhcc
Confidence 468899999999999999874433 5555555777889999999999999998887 4564 455555555554
No 109
>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=27.05 E-value=1.2e+02 Score=23.89 Aligned_cols=60 Identities=18% Similarity=0.282 Sum_probs=44.9
Q ss_pred chHHHHHHHHhhhcccC-ChhHHhhhHHHHHHHHHhhcC--CCcHHHHHHHHHHHHhhhcccC
Q psy10447 31 KGLAAFLKAIGYLIPLM-DAEYANYYTKEVMLILIREFQ--SPDEEMKKIVLKVVKQCCATDG 90 (166)
Q Consensus 31 K~LAaFLKaiG~IIPLM-D~eyA~yYt~evm~il~rEF~--SPDeEMKkiVLkVv~qc~~t~g 90 (166)
..+-.+..++..+.|.. |.-..=|-+..++..+....+ ++|+..-+.+|+.+...|..+.
T Consensus 58 d~~i~~~~~l~~lfp~~~dv~~~l~~~eg~~~~l~~~~~~~~~~~~~~~~~lell~aAc~d~~ 120 (157)
T PF11701_consen 58 DSLIIAFSALTALFPGPPDVGSELFLSEGFLESLLPLASRKSKDRKVQKAALELLSAACIDKS 120 (157)
T ss_dssp CHHHHHHHHHHHHCTTTHHHHHHHCCTTTHHHHHHHHHH-CTS-HHHHHHHHHHHHHHTTSHH
T ss_pred hhHHHHHHHHHHHhCCCHHHHHHHHhhhhHHHHHHHHHhcccCCHHHHHHHHHHHHHHHccHH
Confidence 45555667777788875 444455667788888888888 9999999999999998876654
No 110
>KOG2137|consensus
Probab=26.78 E-value=3e+02 Score=27.82 Aligned_cols=121 Identities=14% Similarity=0.354 Sum_probs=78.7
Q ss_pred hHHHHHHHHhhhcchHHHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhHh
Q psy10447 18 LKPLWKGIRTHRGKGLAAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIK 97 (166)
Q Consensus 18 L~plW~Gir~hRGK~LAaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yir 97 (166)
|.|+.+- .+=++.+.-+++=+-.|+-... +.....-|++.|.|-|++.|--..-.+|+++- -..+-+.-.++|
T Consensus 354 l~pi~~~--~~~~~~~l~i~e~mdlL~~Kt~---~e~~~~~IlplL~~S~~~~~~~iQ~~~L~~lp--tv~e~iD~~~vk 426 (700)
T KOG2137|consen 354 LKPIYSA--SDPKQALLFILENMDLLKEKTP---PEEVKEKILPLLYRSLEDSDVQIQELALQILP--TVAESIDVPFVK 426 (700)
T ss_pred HHHHhcc--CCcccchhhHHhhHHHHHhhCC---hHHHHHHHHHHHHHHhcCcchhhHHHHHHhhh--HHHHhccHHHHH
Confidence 3444433 5666666666666666665554 45678899999999999999999999999887 345566677789
Q ss_pred hhhchHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHhhCHHHHHHHhhcccc
Q psy10447 98 DEILPPFFKNFWNHRMALDRRNYRQLVDTTVEIANKVGASEIINRVVDDLK 148 (166)
Q Consensus 98 ~~i~~~FF~~FW~rR~AlDr~~~~~vv~TTv~lA~Kvg~~~il~~iv~~lK 148 (166)
+.|+|.--.-|-..- -++.+++ +..+--.+++..+..-|++.+...+|
T Consensus 427 ~~ilP~l~~l~~~tt-~~~vkvn--~L~c~~~l~q~lD~~~v~d~~lpi~~ 474 (700)
T KOG2137|consen 427 QAILPRLKNLAFKTT-NLYVKVN--VLPCLAGLIQRLDKAAVLDELLPILK 474 (700)
T ss_pred HHHHHHhhcchhccc-chHHHHH--HHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence 999987655543322 2222221 22333345577777777777666554
No 111
>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=26.71 E-value=75 Score=24.88 Aligned_cols=33 Identities=24% Similarity=0.528 Sum_probs=29.9
Q ss_pred HHHHHHHHhhcCCCcHHHHHHHHHHHHhhhccc
Q psy10447 57 KEVMLILIREFQSPDEEMKKIVLKVVKQCCATD 89 (166)
Q Consensus 57 ~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~ 89 (166)
.|||.-|.+..+..+.--|.-+|||++.||...
T Consensus 37 ~ei~d~L~kRL~~~~~hVK~K~Lrilk~l~~~G 69 (122)
T cd03572 37 QELLEYLLKRLKRSSPHVKLKVLKIIKHLCEKG 69 (122)
T ss_pred HHHHHHHHHHhcCCCCcchHHHHHHHHHHHhhC
Confidence 389999999999999999999999999999875
No 112
>PF15565 Imm16: Immunity protein 16
Probab=26.65 E-value=70 Score=24.67 Aligned_cols=37 Identities=22% Similarity=0.220 Sum_probs=22.7
Q ss_pred hcchHHHHHHHHhhhcccCChhHHh-hhHHHHHHHHHhhcCCCcHH
Q psy10447 29 RGKGLAAFLKAIGYLIPLMDAEYAN-YYTKEVMLILIREFQSPDEE 73 (166)
Q Consensus 29 RGK~LAaFLKaiG~IIPLMD~eyA~-yYt~evm~il~rEF~SPDeE 73 (166)
.+++|.++.+++..+++ .|. ..+ ..+..|.+||++-.
T Consensus 62 ~~~~l~~l~~~~p~m~~-----~A~keWa---~il~~RilNs~~~~ 99 (106)
T PF15565_consen 62 MEEYLPALAEAIPQMMI-----NAPKEWA---KILHYRILNSDDAR 99 (106)
T ss_pred HHHHHHHHHHHHHHHHH-----hhHHHHH---HHHHHHHHcChHHH
Confidence 45666666666666553 333 333 34677899998843
No 113
>PF08445 FR47: FR47-like protein; InterPro: IPR013653 Proteins in this entry have a conserved region similar to the C-terminal region of the Drosophila melanogaster (Fruit fly) hypothetical protein FR47 (Q9VR51 from SWISSPROT). This protein has been found to consist of two N-acyltransferase-like domains swapped with the C-terminal strands. ; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups; PDB: 1SQH_A 3EC4_B.
Probab=25.53 E-value=39 Score=23.81 Aligned_cols=13 Identities=38% Similarity=0.606 Sum_probs=10.5
Q ss_pred HhhhcchHHHHHH
Q psy10447 26 RTHRGKGLAAFLK 38 (166)
Q Consensus 26 r~hRGK~LAaFLK 38 (166)
-.|||||||..|-
T Consensus 31 p~~RrrGlg~~lv 43 (86)
T PF08445_consen 31 PEHRRRGLGSALV 43 (86)
T ss_dssp GGGTTSSHHHHHH
T ss_pred HHHcCCCHHHHHH
Confidence 4799999998764
No 114
>PF08780 NTase_sub_bind: Nucleotidyltransferase substrate binding protein like; InterPro: IPR010235 The member of this family from Haemophilus influenzae, HI0074, has been shown by crystal structure to resemble nucleotidyltransferase substrate binding proteins []. It forms a complex with HI0073 (P43933 from SWISSPROT), encoded by the adjacent gene, which contains a nucleotidyltransferase nucleotide binding domain (IPR002934 from INTERPRO). Double- and single-stranded DNA binding assays showed no evidence of DNA binding to HI0074 or to HI0073/HI0074 complex despite the suggestive shape of the putative binding cleft formed by the HI0074 dimer []. ; PDB: 1WWP_A 1JOG_A 1WTY_C 2YWA_B.
Probab=25.17 E-value=1.2e+02 Score=23.25 Aligned_cols=30 Identities=20% Similarity=0.442 Sum_probs=24.6
Q ss_pred hhhhhhhhHHHHHHHHhhhcchHHHHHHHHhhhcccCCh
Q psy10447 11 IESFDSVLKPLWKGIRTHRGKGLAAFLKAIGYLIPLMDA 49 (166)
Q Consensus 11 IEsFd~VL~plW~Gir~hRGK~LAaFLKaiG~IIPLMD~ 49 (166)
|-.|+-..|-.||-+|. ||+--|.. +..+|
T Consensus 33 IqrFE~t~ElaWK~lK~--------~L~~~G~~-~~~sp 62 (124)
T PF08780_consen 33 IQRFEFTFELAWKTLKD--------YLEYEGIS-ECNSP 62 (124)
T ss_dssp HHHHHHHHHHHHHHHHH--------HHHHCTSS-CCTSH
T ss_pred HHHHHHHHHHHHHHHHH--------HHHHhCCc-ccCCH
Confidence 67899999999988877 88887876 66666
No 115
>PF10948 DUF2635: Protein of unknown function (DUF2635); InterPro: IPR024400 This family consists of uncharacterised proteins found in bacteria and bacteriophages. It includes protein Gp38 from Enterobacteria phage Mu.
Probab=25.07 E-value=37 Score=22.73 Aligned_cols=11 Identities=27% Similarity=0.549 Sum_probs=8.5
Q ss_pred HHHHHHHHhhh
Q psy10447 105 FKNFWNHRMAL 115 (166)
Q Consensus 105 F~~FW~rR~Al 115 (166)
...||.||.+-
T Consensus 27 ~~~yW~RRl~d 37 (47)
T PF10948_consen 27 DTAYWLRRLAD 37 (47)
T ss_pred ccHHHHHhhhc
Confidence 35799999874
No 116
>PF03568 Peptidase_C50: Peptidase family C50; InterPro: IPR005314 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C50 (separase family, clan CD). The active site residues for members of this family and family C14 occur in the same order in the sequence: H,C. The separases are caspase-like proteases, which plays a central role in the chromosome segregation. In yeast they cleave the rad21 subunit of the cohesin complex at the onset of anaphase. During most of the cell cycle, separase is inactivated by the securin/cut2 protein, which probably covers its active site. ; GO: 0008233 peptidase activity, 0006508 proteolysis, 0005634 nucleus
Probab=24.66 E-value=59 Score=29.18 Aligned_cols=19 Identities=42% Similarity=0.649 Sum_probs=16.7
Q ss_pred HHHHHHHhhhhhhhhhHHH
Q psy10447 106 KNFWNHRMALDRRNYRQLV 124 (166)
Q Consensus 106 ~~FW~rR~AlDr~~~~~vv 124 (166)
+.+|.+|-++|.|....+.
T Consensus 68 k~WW~~R~~LD~rL~~LL~ 86 (383)
T PF03568_consen 68 KKWWKERKALDSRLKDLLE 86 (383)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 6799999999999877776
No 117
>KOG1824|consensus
Probab=24.48 E-value=5.9e+02 Score=27.37 Aligned_cols=98 Identities=22% Similarity=0.333 Sum_probs=62.3
Q ss_pred HHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhHhhhhchHHHHHHHHHHhhhh-hhhhhHHH-HHHHHHHHh
Q psy10447 56 TKEVMLILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFKNFWNHRMALD-RRNYRQLV-DTTVEIANK 133 (166)
Q Consensus 56 t~evm~il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~FW~rR~AlD-r~~~~~vv-~TTv~lA~K 133 (166)
..|+-.+++.-|+||.||.|+.----+- ..+-|=-++|+ ||-- .-.-.+ +++|-++. --++--+.+
T Consensus 855 ~~e~~~~iieaf~sp~edvksAAs~ALG--sl~vgnl~~yL------pfil----~qi~sqpk~QyLLLhSlkevi~~~s 922 (1233)
T KOG1824|consen 855 QNELKDTIIEAFNSPSEDVKSAASYALG--SLAVGNLPKYL------PFIL----EQIESQPKRQYLLLHSLKEVIVSAS 922 (1233)
T ss_pred chhhHHHHHHHcCCChHHHHHHHHHHhh--hhhcCchHhHH------HHHH----HHHhcchHhHHHHHHHHHHHHHHhc
Confidence 3444558999999999999997655444 33445566776 3322 222233 45565555 233434555
Q ss_pred hC-----HHHHHHHhhcccccchHHHHHHHHHHHhhc
Q psy10447 134 VG-----ASEIINRVVDDLKDENEQYRKMVMESIEKT 165 (166)
Q Consensus 134 vg-----~~~il~~iv~~lKDesE~~R~M~~eti~kv 165 (166)
++ +..|..-+..+--...|--|..+.|++.|+
T Consensus 923 vd~~~~~v~~IW~lL~k~cE~~eegtR~vvAECLGkL 959 (1233)
T KOG1824|consen 923 VDGLKPYVEKIWALLFKHCECAEEGTRNVVAECLGKL 959 (1233)
T ss_pred cchhhhhHHHHHHHHHHhcccchhhhHHHHHHHhhhH
Confidence 55 556667777777777777799999998874
No 118
>COG4086 Predicted secreted protein [Function unknown]
Probab=23.98 E-value=1.6e+02 Score=26.74 Aligned_cols=81 Identities=20% Similarity=0.341 Sum_probs=54.1
Q ss_pred hhhcccCcchhhHhhhhchHH-----------HHHHHHH----HhhhhhhhhhHHHHHHHHHHHhhCHHH---------H
Q psy10447 84 QCCATDGVEAQYIKDEILPPF-----------FKNFWNH----RMALDRRNYRQLVDTTVEIANKVGASE---------I 139 (166)
Q Consensus 84 qc~~t~gv~~~yir~~i~~~F-----------F~~FW~r----R~AlDr~~~~~vv~TTv~lA~Kvg~~~---------i 139 (166)
+...|-|+.+.++ .+-.|| +++|=.- =.--++|-+.+...+|-||++|.|... |
T Consensus 123 nAL~TaGi~~a~V--~VtaP~pvSGeAALaGv~KayE~a~g~~Ipe~~KqvaneEL~~~sel~~k~G~d~~r~a~l~~~V 200 (299)
T COG4086 123 NALVTAGIEDAKV--TVTAPFPVSGEAALAGVYKAYEAAVGVQIPEANKQVANEELVATSELGDKIGDDPRRAAALMAEV 200 (299)
T ss_pred HHHHhcCCCCceE--EEecCccCccHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHHHhhhhcCCCHHHHHHHHHHH
Confidence 4445667776665 444454 5666322 011357788888899999999999654 5
Q ss_pred HHHhhcccccchHHHHHHHHHHHhhcC
Q psy10447 140 INRVVDDLKDENEQYRKMVMESIEKTN 166 (166)
Q Consensus 140 l~~iv~~lKDesE~~R~M~~eti~kv~ 166 (166)
-+++...=-|.-+..|+.+-++.+..|
T Consensus 201 K~~~a~~~~~~~~dirkvv~dv~~~yn 227 (299)
T COG4086 201 KEEVAKQKVDDPADIRKVVDDVANNYN 227 (299)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHHcC
Confidence 555555545677889999988877654
No 119
>PF11919 DUF3437: Domain of unknown function (DUF3437); InterPro: IPR021843 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 142 to 163 amino acids in length. ; PDB: 3L5Q_6 1VSY_5.
Probab=23.58 E-value=91 Score=23.09 Aligned_cols=37 Identities=32% Similarity=0.452 Sum_probs=22.3
Q ss_pred HHhhhc-chHHHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCC
Q psy10447 25 IRTHRG-KGLAAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQS 69 (166)
Q Consensus 25 ir~hRG-K~LAaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~S 69 (166)
+++|-| -||+||+.|.=|-+|. |.-+++..|.+-=++
T Consensus 4 ~~rH~~VLGL~Alv~a~Py~vP~--------w~P~~l~~La~~~~~ 41 (90)
T PF11919_consen 4 RRRHAAVLGLSALVLAFPYDVPP--------WMPEVLEELARHAND 41 (90)
T ss_dssp HHHHHHHHHHHHHHTT-S--SS---------HHHHHHHHHHTTSSS
T ss_pred HHHHHHHHHHHHHHHHcCCCCcc--------cHHHHHHHHHHHhCC
Confidence 344544 4889999999888887 677777766654443
No 120
>KOG4215|consensus
Probab=23.37 E-value=4e+02 Score=25.45 Aligned_cols=86 Identities=20% Similarity=0.349 Sum_probs=57.0
Q ss_pred HHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCc----HHHHHHHHHHHHhhhcccCc-c-----hhhHhhhhchH
Q psy10447 34 AAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPD----EEMKKIVLKVVKQCCATDGV-E-----AQYIKDEILPP 103 (166)
Q Consensus 34 AaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPD----eEMKkiVLkVv~qc~~t~gv-~-----~~yir~~i~~~ 103 (166)
=++||||.+.=|. .+..++|- +|||-.||+-+..-+....- + .+-+ -++|.
T Consensus 258 y~cLKAi~FfdP~-----------------akGis~~s~~~I~~aR~~vl~sLe~yi~d~q~~d~~~R~g~LL--LllPs 318 (432)
T KOG4215|consen 258 YVCLKAIAFFDPD-----------------AKGLSDPSQIRIREARNRVLKSLEAYISDRQPYDAPGRFGNLL--LLLPS 318 (432)
T ss_pred HHHHHHHHhcCcc-----------------ccccCCchHhHHHHHHHHHHHHHHHHHhhcCccccccchhhHH--HHHHH
Confidence 3589999988664 33444444 89999999988865544331 1 1111 23332
Q ss_pred HHHHHHHHHhhhhhhhhhHHHHHHHHHHHhhCHHHHHHHhhcccccch
Q psy10447 104 FFKNFWNHRMALDRRNYRQLVDTTVEIANKVGASEIINRVVDDLKDEN 151 (166)
Q Consensus 104 FF~~FW~rR~AlDr~~~~~vv~TTv~lA~Kvg~~~il~~iv~~lKDes 151 (166)
- .....++||- +.||+=+|.+.|...+-+.++++.
T Consensus 319 L------------qsIt~qliE~-iqlaklFGla~vDsll~e~~l~~~ 353 (432)
T KOG4215|consen 319 L------------QSITQQLIEQ-IQLAKLFGLAKVDSLLQEFLLGGE 353 (432)
T ss_pred H------------HHHHHHHHHH-HHHHHHhhhhhHhHHHHHhhcCCC
Confidence 2 2356677776 669999999999999998888754
No 121
>PF11423 Repressor_Mnt: Regulatory protein Mnt; InterPro: IPR024421 Mnt is a repressor which is involved in the genetic switch between lysogenic and lytic growth in bacteriophage P22. The C-terminal domain of the protein consists of a dimer of two antiparallel coiled coils with a right handed twist, which is both stronger and has closer inter-helical separation compared with those found in left-handed coiled coils []. This entry is represented by Bacteriophage P22, Mnt. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 1QEY_C 1MNT_B.
Probab=22.99 E-value=70 Score=19.98 Aligned_cols=16 Identities=31% Similarity=0.590 Sum_probs=12.8
Q ss_pred chHHHHHHHHHHHhhc
Q psy10447 150 ENEQYRKMVMESIEKT 165 (166)
Q Consensus 150 esE~~R~M~~eti~kv 165 (166)
.||.+.+||.||+..+
T Consensus 11 qse~vkk~VfetLK~~ 26 (30)
T PF11423_consen 11 QSEMVKKMVFETLKDM 26 (30)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4788999999988653
No 122
>PF07725 LRR_3: Leucine Rich Repeat; InterPro: IPR011713 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []. LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. This entry includes some LRRs that fail to be detected by the IPR001611 from INTERPRO model.
Probab=22.80 E-value=19 Score=20.39 Aligned_cols=11 Identities=45% Similarity=1.117 Sum_probs=8.3
Q ss_pred hhhHHHHHHHH
Q psy10447 16 SVLKPLWKGIR 26 (166)
Q Consensus 16 ~VL~plW~Gir 26 (166)
+=++-||+|++
T Consensus 10 S~lekLW~G~k 20 (20)
T PF07725_consen 10 SKLEKLWEGVK 20 (20)
T ss_pred CChHHhcCccC
Confidence 34789999974
No 123
>PF05099 TerB: Tellurite resistance protein TerB; InterPro: IPR007791 The prokaryotic heat shock protein DnaJ interacts with the chaperone hsp70-like DnaK protein []. Structurally, the DnaJ protein consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acids, a glycine-rich region ('G' domain') of about 30 residues, a central domain containing four repeats of a CXXCXGXG motif ('CRR' domain) and a C-terminal region of 120 to 170 residues. Direct interaction between DnaK and djlA is needed for the induction of the wcaABCDE operon which is involved in the synthesis of a colanic acid polysaccharide capsule. The colanic acid capsule may help the bacterium survive conditions outside the host [, ]; PDB: 2H5N_D 2JXU_A.
Probab=22.54 E-value=3.2e+02 Score=20.00 Aligned_cols=81 Identities=15% Similarity=0.311 Sum_probs=47.2
Q ss_pred HHHHHHHHHhhhcccCcchhhHhhhhchHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHh-hCHHHHHHHhhcccccc-hH
Q psy10447 75 KKIVLKVVKQCCATDGVEAQYIKDEILPPFFKNFWNHRMALDRRNYRQLVDTTVEIANK-VGASEIINRVVDDLKDE-NE 152 (166)
Q Consensus 75 KkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~FW~rR~AlDr~~~~~vv~TTv~lA~K-vg~~~il~~iv~~lKDe-sE 152 (166)
+..++.++-.+...||....=-++.+. .++ ..+..++......+.+....+.++ .+..+.+.. +++. ++
T Consensus 23 ~~a~~~ll~~~a~aDG~v~~~E~~~i~-~~~----~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~----l~~~~~~ 93 (140)
T PF05099_consen 23 REALLALLAAVAKADGEVDPEEIEAIR-QLL----AERFGLSPEEAEELIELADELKQEPIDLEELLRE----LRDSLSP 93 (140)
T ss_dssp HHHHHHHHHHHHHTTSS--CHHHHHHH-HHH----HHCGCGSCHHHHHHHHHHCHHHHHCCHHHHHHHH----HCTS--H
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHH-HHH----HHhhCCCHHHHHHHHHHHHHHHhccccHHHHHHH----HHHhhch
Confidence 999999999999999976654333332 333 344455554555666555555555 444444443 4442 46
Q ss_pred HHHHHHHHHHhh
Q psy10447 153 QYRKMVMESIEK 164 (166)
Q Consensus 153 ~~R~M~~eti~k 164 (166)
..|..+++.+-.
T Consensus 94 ~~r~~ll~~l~~ 105 (140)
T PF05099_consen 94 EEREDLLRMLIA 105 (140)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 777777776544
No 124
>PF06902 Fer4_19: Divergent 4Fe-4S mono-cluster; InterPro: IPR010693 This entry represents bacterial ferredoxins such Ferredoxin-1, -2 and -soy from Streptomyces griseolus and Ferredoxin fas2 from Rhodococcus fascians, plus several bacterial hypothetical proteins that contain three highly conserved cysteine residues. These ferredoxins each bind a 3Fe-4S cluster. Ferredoxin-soy (SoyB) act as electron transport protein for the cytochrome P450-SOY system []. Ferredoxin-1 (SuaB) and Ferredoxin-2 (SubB) act as electron transport proteins for the herbicide-metabolising cytochrome P-450 SU1 and SU2 systems, respectively [, ]. Ferredoxin-fas2 also plays a role in electrontransfer, the fas operon encoding genes involved in cytokinin production and in host plant fasciation (leafy gall).
Probab=22.53 E-value=46 Score=23.13 Aligned_cols=20 Identities=35% Similarity=0.519 Sum_probs=18.7
Q ss_pred CCcHHHHHHHHHHHHhhhcc
Q psy10447 69 SPDEEMKKIVLKVVKQCCAT 88 (166)
Q Consensus 69 SPDeEMKkiVLkVv~qc~~t 88 (166)
+||++-...|.+++.+|++.
T Consensus 38 ~~d~a~~~~v~~~v~~CPSG 57 (64)
T PF06902_consen 38 SPDEASAEEVREAVDRCPSG 57 (64)
T ss_pred CcCccCHHHHHHHHHcCCcc
Confidence 89999999999999999974
No 125
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=22.30 E-value=2.1e+02 Score=28.24 Aligned_cols=82 Identities=15% Similarity=0.268 Sum_probs=50.4
Q ss_pred cchhhhhhhhHHHHHHHHhhhcchHHHHHHHHhhhcccCChhHHhhhHHHHHHHHH-hhcCCCcHHHHHHH---HHHHHh
Q psy10447 9 LSIESFDSVLKPLWKGIRTHRGKGLAAFLKAIGYLIPLMDAEYANYYTKEVMLILI-REFQSPDEEMKKIV---LKVVKQ 84 (166)
Q Consensus 9 YGIEsFd~VL~plW~Gir~hRGK~LAaFLKaiG~IIPLMD~eyA~yYt~evm~il~-rEF~SPDeEMKkiV---LkVv~q 84 (166)
+|-.|.+ -||..|...|+.-|..||.|+| ||..-+.-|. .|. +.|.|=+. ..... ..-..+
T Consensus 478 ~geksa~----nl~~~Ie~sk~~~l~r~l~ALG--I~~vG~~~ak--------~La~~~f~~~~~-l~~~~~~~~~~~e~ 542 (669)
T PRK14350 478 FKDKRIN----NLKRSIEASKKRPFSKLLLSMG--IKDLGENTIL--------LLINNNLNSFDK-ISTLCQDREFALSK 542 (669)
T ss_pred ccHHHHH----HHHHHHHHHhCCCHHHHHHHcC--CCchhHHHHH--------HHHHHhhCCHHH-HHhhhhccCCCHHH
Confidence 3444444 5888999999999999999999 7876543332 455 56655332 21110 012345
Q ss_pred hhcccCcchhhHhhhhchHHHHH
Q psy10447 85 CCATDGVEAQYIKDEILPPFFKN 107 (166)
Q Consensus 85 c~~t~gv~~~yir~~i~~~FF~~ 107 (166)
+..-+|+.+.- -+.|. .||..
T Consensus 543 l~~i~giG~~~-a~si~-~ff~~ 563 (669)
T PRK14350 543 LLKIKGIGEKI-ALNII-EAFND 563 (669)
T ss_pred HhhCCCccHHH-HHHHH-HHHcC
Confidence 67778888864 33333 57654
No 126
>TIGR02412 pepN_strep_liv aminopeptidase N, Streptomyces lividans type. This family is a subset of the members of the zinc metallopeptidase family M1 (pfam01433), with a single member characterized in Streptomyces lividans 66 and designated aminopeptidase N. The spectrum of activity may differ somewhat from the aminopeptidase N clade of E. coli and most other Proteobacteria, well separated phylogenetically within the M1 family. The M1 family also includes leukotriene A-4 hydrolase/aminopeptidase (with a bifunctional active site).
Probab=21.52 E-value=4.9e+02 Score=25.95 Aligned_cols=69 Identities=9% Similarity=0.126 Sum_probs=34.8
Q ss_pred hhhhchHHHHHHHHHHhhhhhhhhhHHHHHHHHHHH--hhCHHHHHHHhhccc---ccchHHHHHHHHHHHhhc
Q psy10447 97 KDEILPPFFKNFWNHRMALDRRNYRQLVDTTVEIAN--KVGASEIINRVVDDL---KDENEQYRKMVMESIEKT 165 (166)
Q Consensus 97 r~~i~~~FF~~FW~rR~AlDr~~~~~vv~TTv~lA~--Kvg~~~il~~iv~~l---KDesE~~R~M~~eti~kv 165 (166)
..+++-+|++.+|.+=.....+..-.+....+...- -.-..+.++.+-..+ ++....+||.+.++.+.+
T Consensus 749 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~r~l~~~~d~~ 822 (831)
T TIGR02412 749 QALLLAAYAERYFANLADIWKRRGPAIAQAISRGLFPATAVNYDTLATADKWLRSQADASPGLRRTLLERRDAA 822 (831)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHhcCCcccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhHH
Confidence 356677899999975333322211111111110000 111234444444455 466788999999887653
No 127
>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=21.41 E-value=3.1e+02 Score=19.55 Aligned_cols=66 Identities=15% Similarity=0.228 Sum_probs=46.8
Q ss_pred hhhhchHHHHHHHHHHhhhhhhhhhHHHHHHHHHHH------hhCHHHHHHHhhcccccchHHHHHHHHHHHhhc
Q psy10447 97 KDEILPPFFKNFWNHRMALDRRNYRQLVDTTVEIAN------KVGASEIINRVVDDLKDENEQYRKMVMESIEKT 165 (166)
Q Consensus 97 r~~i~~~FF~~FW~rR~AlDr~~~~~vv~TTv~lA~------Kvg~~~il~~iv~~lKDesE~~R~M~~eti~kv 165 (166)
..+++.||=.=| +++ .+.....++++...++-+ |-|=..|++=+-.-.+|++|++=++|.++++.|
T Consensus 15 Q~~fL~Pf~~i~--~~~-~~~~vre~il~ci~qil~~~~~~i~SGW~~if~il~~aa~~~~e~lv~~af~~~~~I 86 (86)
T PF09324_consen 15 QKDFLKPFEYIM--SNN-PSIDVRELILECILQILQSRGENIKSGWKVIFSILRAAAKDNDESLVRLAFQIVQLI 86 (86)
T ss_pred HHHHHHHHHHHH--hcc-CcHHHHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHhCCCccHHHHHHHHHhhC
Confidence 566777776555 222 444444555566555554 567778888888888999999999999998865
No 128
>PF14198 TnpV: Transposon-encoded protein TnpV
Probab=21.36 E-value=2e+02 Score=22.00 Aligned_cols=57 Identities=21% Similarity=0.337 Sum_probs=40.4
Q ss_pred HHHhhcCCCcHHHHHHHHHHHHhhhcccCcchhhHhhhhchHHHHHHHHHHhhhhhhhhhHHH
Q psy10447 62 ILIREFQSPDEEMKKIVLKVVKQCCATDGVEAQYIKDEILPPFFKNFWNHRMALDRRNYRQLV 124 (166)
Q Consensus 62 il~rEF~SPDeEMKkiVLkVv~qc~~t~gv~~~yir~~i~~~FF~~FW~rR~AlDr~~~~~vv 124 (166)
.|-.....=|++-..-+-++++|+...+||+-+-=.++-+ =|++||-.-|-....+|
T Consensus 50 ~L~~~l~eid~~A~e~~e~l~~q~~~~~gvtE~LK~~dqm------~wv~~mN~ir~~AeEiV 106 (111)
T PF14198_consen 50 KLNEHLAEIDEQAQERFERLVEQMAEKEGVTEELKAEDQM------EWVRRMNNIRAQAEEIV 106 (111)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcHhhhhcCHH------HHHHHHHHHHHHHHHHH
Confidence 3444555568888888999999999999999642122222 29999988776666555
No 129
>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=21.01 E-value=1.8e+02 Score=22.87 Aligned_cols=33 Identities=24% Similarity=0.416 Sum_probs=26.3
Q ss_pred HHHhhCHHHHHHHhhcccccchHHHHHHHHHHHhhc
Q psy10447 130 IANKVGASEIINRVVDDLKDENEQYRKMVMESIEKT 165 (166)
Q Consensus 130 lA~Kvg~~~il~~iv~~lKDesE~~R~M~~eti~kv 165 (166)
+.++.|+.+.|-.++. ++++..|+=|+.|++|+
T Consensus 81 ii~~lg~K~~vM~Lm~---h~d~eVr~eAL~avQkl 113 (119)
T PF11698_consen 81 IIEKLGAKERVMELMN---HEDPEVRYEALLAVQKL 113 (119)
T ss_dssp HHHHHSHHHHHHHHTS----SSHHHHHHHHHHHHHH
T ss_pred HHHhcChHHHHHHHhc---CCCHHHHHHHHHHHHHH
Confidence 3478898887777766 48999999999999874
No 130
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=20.74 E-value=1.7e+02 Score=19.72 Aligned_cols=38 Identities=24% Similarity=0.397 Sum_probs=29.1
Q ss_pred HHHHHhhCHH-HHHHHhhcccccchHHHHHHHHHHHhhc
Q psy10447 128 VEIANKVGAS-EIINRVVDDLKDENEQYRKMVMESIEKT 165 (166)
Q Consensus 128 v~lA~Kvg~~-~il~~iv~~lKDesE~~R~M~~eti~kv 165 (166)
-+||++.|++ .-|.+++++-..=+++-|.-+.+++.++
T Consensus 4 ~~iA~~~gvS~~TVSr~ln~~~~v~~~t~~~i~~~~~~~ 42 (70)
T smart00354 4 KDVARLAGVSKATVSRVLNGNGRVSEETREKVLAAMEEL 42 (70)
T ss_pred HHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHh
Confidence 4688888875 4778888876666788888888887765
No 131
>PRK00865 glutamate racemase; Provisional
Probab=20.63 E-value=84 Score=26.53 Aligned_cols=29 Identities=7% Similarity=-0.085 Sum_probs=24.8
Q ss_pred CccccCCcchhhhhhhhHHHHHHHHhhhc
Q psy10447 2 TDIHCHTLSIESFDSVLKPLWKGIRTHRG 30 (166)
Q Consensus 2 ~~~as~PYGIEsFd~VL~plW~Gir~hRG 30 (166)
.|.+-.|||..+-+.+.+-+.+.++.-.-
T Consensus 37 ~D~~~~PYG~ks~~~i~~~~~~~~~~L~~ 65 (261)
T PRK00865 37 GDTARFPYGEKSEEEIRERTLEIVEFLLE 65 (261)
T ss_pred ecCCCCCCCCCCHHHHHHHHHHHHHHHHh
Confidence 58899999999999999998888776544
No 132
>PF04104 DNA_primase_lrg: Eukaryotic and archaeal DNA primase, large subunit; InterPro: IPR007238 DNA primase is the polymerase that synthesises small RNA primers for the Okazaki fragments made during discontinuous DNA replication. DNA primase is a heterodimer of two subunits, the small subunit Pri1 (48 kDa in yeast), and the large subunit Pri2 (58 kDa in the yeast Saccharomyces cerevisiae) []. Both subunits participate in the formation of the active site, but the ATP binding site is located on the small subunit []. Primase function has also been demonstrated for human and mouse primase subunits [].; GO: 0003896 DNA primase activity, 0006269 DNA replication, synthesis of RNA primer; PDB: 1ZT2_B 3Q36_A 3L9Q_B 2DLA_B 3LGB_B.
Probab=20.62 E-value=36 Score=28.99 Aligned_cols=72 Identities=26% Similarity=0.482 Sum_probs=46.8
Q ss_pred hhhhhhhHHHHHHHHh-----hhcc-hHHHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHHHhh
Q psy10447 12 ESFDSVLKPLWKGIRT-----HRGK-GLAAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVVKQC 85 (166)
Q Consensus 12 EsFd~VL~plW~Gir~-----hRGK-~LAaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv~qc 85 (166)
++|=|-+.-|..++++ |.|+ .|++|||.||.-+ .|++.....+|+..+++..|...=-|+-.
T Consensus 106 ~~FPpCMr~l~~~L~~~~hL~h~~R~ql~lFLk~iGl~~------------ee~l~f~~~~f~~~~~~F~k~~~Y~IrH~ 173 (260)
T PF04104_consen 106 ESFPPCMRNLHERLRKGHHLKHSGRFQLGLFLKGIGLSL------------EEALEFWRSEFSKSAPDFDKEYRYNIRHI 173 (260)
T ss_dssp CCS-HHHHHHHHHHHHHS---HHHHHHHHHHHHHTTEEC------------CCHHHCCHHHCCT-HHHHHHHTHCCCCCH
T ss_pred ccCChHHHHHHHHHhhCCCCCchhHhhHHHHHHhcCCCH------------HHHHHHHHHHhccCcHhHHHHhHhhhhhh
Confidence 5788888889888854 4454 6999999999764 56777777888887777777444345555
Q ss_pred hcccCcchhh
Q psy10447 86 CATDGVEAQY 95 (166)
Q Consensus 86 ~~t~gv~~~y 95 (166)
-+-+|=..+|
T Consensus 174 yG~eG~r~~Y 183 (260)
T PF04104_consen 174 YGLEGKRTNY 183 (260)
T ss_dssp TT-STT----
T ss_pred ccCCCCCeee
Confidence 5555555554
No 133
>COG1317 FliH Flagellar biosynthesis/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=20.48 E-value=3e+02 Score=23.45 Aligned_cols=76 Identities=28% Similarity=0.262 Sum_probs=48.9
Q ss_pred HHhhhcccCcchhhHhh---hhchHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHhhCHHHHHHHhhcccccchHHHHHHH
Q psy10447 82 VKQCCATDGVEAQYIKD---EILPPFFKNFWNHRMALDRRNYRQLVDTTVEIANKVGASEIINRVVDDLKDENEQYRKMV 158 (166)
Q Consensus 82 v~qc~~t~gv~~~yir~---~i~~~FF~~FW~rR~AlDr~~~~~vv~TTv~lA~Kvg~~~il~~iv~~lKDesE~~R~M~ 158 (166)
-.|.-..+|-...+..- +=+..-...|=+..-+++++..++++....++|+|| |-..+.+.++.+..++
T Consensus 75 g~q~G~~eG~~~g~~~~~~~e~~~~li~~~~~~~~~~~~~~e~qLv~lvl~ia~~V--------i~~~~~~~~~~ll~~v 146 (234)
T COG1317 75 GFQLGYEEGFEEGQEEGRVLERLAKLIAEFQAELEALKEVVEKQLVQLVLEIARKV--------IGKELELDPEALLAAV 146 (234)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HhHHHhcCHHHHHHHH
Confidence 33444455555555321 222334556666777777888999999999999865 2233455667788888
Q ss_pred HHHHhhc
Q psy10447 159 MESIEKT 165 (166)
Q Consensus 159 ~eti~kv 165 (166)
-++++++
T Consensus 147 ~e~L~~~ 153 (234)
T COG1317 147 REALEEV 153 (234)
T ss_pred HHHHHhc
Confidence 8887754
No 134
>cd06867 PX_SNX41_42 The phosphoinositide binding Phox Homology domain of fungal Sorting Nexins 41 and 42. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX41 and SNX42 (also called Atg20p) form dimers with SNX4, and are required in protein recycling from the sorting endosome (post-Golgi endosome) back
Probab=20.47 E-value=1.1e+02 Score=22.49 Aligned_cols=21 Identities=24% Similarity=0.309 Sum_probs=15.7
Q ss_pred HhhhcchHHHHHHHHhhhcccC
Q psy10447 26 RTHRGKGLAAFLKAIGYLIPLM 47 (166)
Q Consensus 26 r~hRGK~LAaFLKaiG~IIPLM 47 (166)
-..|-++|..||+.|... |.+
T Consensus 79 ie~Rr~~Le~fL~~l~~~-p~l 99 (112)
T cd06867 79 IERRKRMLQRFLNRCLQH-PIL 99 (112)
T ss_pred HHHHHHHHHHHHHHHhcC-hhh
Confidence 466778999999999644 433
No 135
>PF09209 DUF1956: Domain of unknown function (DUF1956); InterPro: IPR015292 This entry represents the C-terminal domain found in the hypothetical transcriptional regulator YbiH from bacteria such as Salmonella typhimurium and Escherichia coli. YbiH is a member of the TetR (tetracycline resistance) transcriptional regulator family of proteins. The C-terminal domains of YbiH and TetR share a multi-helical, interlocking structure.; PDB: 1T33_A.
Probab=20.43 E-value=2.3e+02 Score=20.12 Aligned_cols=44 Identities=23% Similarity=0.498 Sum_probs=24.0
Q ss_pred HHHHHHHHhhhcccCChhHHhhhHHHHHHHHHhhcCCCcHHHHHHHHHHH
Q psy10447 33 LAAFLKAIGYLIPLMDAEYANYYTKEVMLILIREFQSPDEEMKKIVLKVV 82 (166)
Q Consensus 33 LAaFLKaiG~IIPLMD~eyA~yYt~evm~il~rEF~SPDeEMKkiVLkVv 82 (166)
|-+|++++-.- +.+++.+..+ ++++.||..+|.+-...++-+.+
T Consensus 5 L~~~i~~~~~~--l~~~~~~~~~----~~l~~RE~~~Pt~~~~~i~~~~~ 48 (125)
T PF09209_consen 5 LRAFIRALLRR--LLSDPESRWW----LRLIAREMLNPTPAFDRIVEELI 48 (125)
T ss_dssp HHHHHHHHHHH--TTSG-GGHHH----HHHHHHHHHS--HHHHHHHHHTH
T ss_pred HHHHHHHHHHH--HHcccchhHH----HHHHHHHhcCchHHHHHHHHHHh
Confidence 44455544332 4555445554 45778888888888776654443
No 136
>PF00583 Acetyltransf_1: Acetyltransferase (GNAT) family; InterPro: IPR000182 The N-acetyltransferases (NAT) (EC 2.3.1.-) are enzymes that use acetyl coenzyme A (CoA) to transfer an acetyl group to a substrate, a reaction implicated in various functions from bacterial antibiotic resistance to mammalian circadian rhythm and chromatin remodeling. The Gcn5-related N-acetyltransferases (GNAT) catalyze the transfer of the acetyl from the CoA donor to a primary amine of the acceptor. The GNAT proteins share a domain composed of four conserved sequence motifs A-D [, ]. This GNAT domain is named after yeast GCN5 (from General Control Nonrepressed) and related histone acetyltransferases (HATs) like Hat1 and PCAF. HATs acetylate lysine residues of amino terminal histone tails, resulting in transcription activation. Another category of GNAT, the aminoglycoside N-acetyltransferases, confer antibiotic resistance by catalyzing the acetylation of amino groups in aminoglycoside antibiotics []. GNAT proteins can also have anabolic and catabolic functions in both prokaryotes and eukaryotes [, , , , ]. The acetyltransferase/GNAT domain forms a structurally conserved fold of 6 to 7 beta strands (B) and 4 helices (H) in the topology B1-H1-H2-B2-B3-B4-H3-B5-H4-B6, followed by a C-terminal strand which may be from the same monomer or contributed by another [, ]. Motifs D (B2-B3), A (B4-H3) and B (B5-H4) are collectively called the HAT core [, , ], while the N-terminal motif C (B1-H1) is less conserved. Some proteins known to contain a GNAT domain: Yeast GCN5 and Hat1, which are histone acetyltransferases (EC 2.3.1.48). Human PCAF, a histone acetyltransferase. Mammalian serotonin N-acetyltransferase (SNAT) or arylalkylamine NAT (AANAT), which acetylates serotonin into a circadian neurohormone that may participate in light-dark rhythms, and human mood and behavior. Mammalian glucosamine 6-phosphate N-acetyltransferase (GNA1) (EC 2.3.1.4). Escherichia coli rimI and rimJ, which acetylate the N-terminal alanine of ribosomal proteins S18 and S5, respectively (EC 2.3.1.128). Mycobacterium tuberculosis aminoglycoside 2'-N-acetyltransferase (aac), which acetylates the 2' hydroxyl or amino group of a broad spectrum of aminoglycoside antibiotics. Bacillus subtilis bltD and paiA, which acetylate spermine and spermidine. This entry represents the entire GNAT domain.; GO: 0008080 N-acetyltransferase activity, 0008152 metabolic process; PDB: 3T9Y_A 2R7H_B 2OZH_A 1Y9W_B 1VKC_B 2OH1_C 3R9E_B 3R9G_B 3R9F_A 3R96_A ....
Probab=20.39 E-value=61 Score=20.80 Aligned_cols=13 Identities=31% Similarity=0.493 Sum_probs=9.8
Q ss_pred HhhhcchHHHHHH
Q psy10447 26 RTHRGKGLAAFLK 38 (166)
Q Consensus 26 r~hRGK~LAaFLK 38 (166)
.+|||++++..|-
T Consensus 35 ~~~r~~Gig~~L~ 47 (83)
T PF00583_consen 35 PEYRGQGIGSKLL 47 (83)
T ss_dssp GGGTTSSHHHHHH
T ss_pred HHHhhCCCchhhh
Confidence 4789998887663
No 137
>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A.
Probab=20.13 E-value=1.3e+02 Score=19.91 Aligned_cols=35 Identities=23% Similarity=0.345 Sum_probs=23.2
Q ss_pred CcHHHHHHHHHHHHhhhcccC-cchhhHhhhhchHH
Q psy10447 70 PDEEMKKIVLKVVKQCCATDG-VEAQYIKDEILPPF 104 (166)
Q Consensus 70 PDeEMKkiVLkVv~qc~~t~g-v~~~yir~~i~~~F 104 (166)
++++.++.|.+++.+....+| +...-+...+...|
T Consensus 2 ~~~~~~~~l~~ll~~~~~~~g~v~ls~l~~~~~~~~ 37 (74)
T PF12872_consen 2 SLEELKKLLRELLESQKGEDGWVSLSQLGQEYKKKY 37 (74)
T ss_dssp --HHHHHHHHHHHHHTCTTTSSEEHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHhCcCCCceEEHHHHHHHHHHHC
Confidence 467888899999977777665 77666655555444
Done!