Query 005358
Match_columns 700
No_of_seqs 129 out of 147
Neff 4.4
Searched_HMMs 46136
Date Thu Mar 28 22:12:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005358.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005358hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd03572 ENTH_epsin_related ENT 100.0 4.4E-45 9.6E-50 338.6 13.0 121 12-133 1-121 (122)
2 PF01417 ENTH: ENTH domain; I 99.9 4.8E-27 1E-31 216.8 9.8 114 15-132 6-122 (125)
3 cd03571 ENTH_epsin ENTH domain 99.9 3.6E-23 7.7E-28 192.8 10.5 114 15-133 4-120 (123)
4 KOG2056 Equilibrative nucleosi 99.8 6.6E-21 1.4E-25 201.9 10.5 116 14-134 23-141 (336)
5 smart00273 ENTH Epsin N-termin 99.6 7.6E-16 1.6E-20 142.7 11.4 115 15-132 5-120 (127)
6 cd00197 VHS_ENTH_ANTH VHS, ENT 99.6 8.9E-16 1.9E-20 139.4 11.5 113 15-131 3-115 (115)
7 KOG2057 Predicted equilibrativ 99.6 4.9E-15 1.1E-19 155.7 9.5 129 3-134 13-146 (499)
8 cd03564 ANTH_AP180_CALM ANTH d 99.0 2.2E-09 4.8E-14 98.7 9.9 112 15-129 3-114 (117)
9 smart00288 VHS Domain present 98.2 8.8E-06 1.9E-10 76.9 10.1 109 15-131 3-111 (133)
10 cd03568 VHS_STAM VHS domain fa 98.1 2.1E-05 4.5E-10 75.8 10.5 108 15-131 3-110 (144)
11 cd03561 VHS VHS domain family; 98.1 3.2E-05 7E-10 72.9 10.6 107 15-131 3-112 (133)
12 PF00790 VHS: VHS domain; Int 98.0 2.7E-05 5.9E-10 73.9 10.1 108 15-130 8-117 (140)
13 PF01417 ENTH: ENTH domain; I 98.0 5E-05 1.1E-09 70.7 11.2 106 269-380 4-122 (125)
14 cd03567 VHS_GGA VHS domain fam 98.0 5.4E-05 1.2E-09 72.7 11.0 110 15-131 4-116 (139)
15 cd03569 VHS_Hrs_Vps27p VHS dom 97.8 0.00016 3.5E-09 69.4 10.8 108 15-131 7-114 (142)
16 cd00197 VHS_ENTH_ANTH VHS, ENT 97.8 0.00056 1.2E-08 62.4 13.1 101 271-377 3-113 (115)
17 cd03571 ENTH_epsin ENTH domain 97.7 0.00051 1.1E-08 64.9 12.1 105 271-381 4-120 (123)
18 cd03565 VHS_Tom1 VHS domain fa 97.6 0.00035 7.6E-09 67.1 10.2 110 15-131 4-115 (141)
19 PF07651 ANTH: ANTH domain; I 97.5 0.00025 5.3E-09 73.6 7.5 114 15-130 6-121 (280)
20 KOG2199 Signal transducing ada 97.3 0.0016 3.5E-08 71.7 10.9 111 15-133 11-123 (462)
21 KOG2056 Equilibrative nucleosi 97.2 0.0012 2.6E-08 71.6 9.3 96 285-384 36-143 (336)
22 KOG1087 Cytosolic sorting prot 97.1 0.0027 5.8E-08 71.9 10.9 109 15-131 4-112 (470)
23 KOG0251 Clathrin assembly prot 96.7 0.0068 1.5E-07 69.1 10.0 114 15-131 26-140 (491)
24 smart00273 ENTH Epsin N-termin 96.7 0.032 6.8E-07 52.1 12.5 105 269-380 4-120 (127)
25 cd03572 ENTH_epsin_related ENT 96.3 0.023 5E-07 54.0 9.0 86 289-379 23-119 (122)
26 cd03568 VHS_STAM VHS domain fa 95.9 0.073 1.6E-06 51.6 10.3 93 289-383 16-114 (144)
27 PF00790 VHS: VHS domain; Int 95.5 0.11 2.4E-06 49.5 10.1 105 270-382 7-121 (140)
28 cd03561 VHS VHS domain family; 95.5 0.29 6.3E-06 46.3 12.6 109 271-384 3-117 (133)
29 smart00288 VHS Domain present 95.4 0.38 8.2E-06 45.8 13.1 108 271-383 3-115 (133)
30 cd03567 VHS_GGA VHS domain fam 94.7 0.67 1.4E-05 44.9 12.9 107 271-382 4-119 (139)
31 cd03569 VHS_Hrs_Vps27p VHS dom 94.7 0.64 1.4E-05 45.0 12.7 110 271-384 7-119 (142)
32 cd03565 VHS_Tom1 VHS domain fa 93.9 0.6 1.3E-05 45.1 10.6 107 270-383 3-119 (141)
33 PF12717 Cnd1: non-SMC mitotic 90.4 1.2 2.5E-05 44.0 8.1 82 36-132 12-93 (178)
34 PF12348 CLASP_N: CLASP N term 89.6 1.8 3.8E-05 43.4 8.8 89 289-379 116-206 (228)
35 cd03562 CID CID (CTD-Interacti 89.1 3.2 6.9E-05 37.9 9.4 106 269-381 4-110 (114)
36 PF12755 Vac14_Fab1_bd: Vacuol 87.7 4.8 0.0001 36.7 9.4 73 302-378 24-96 (97)
37 KOG1818 Membrane trafficking a 87.6 1.9 4.2E-05 50.9 8.5 108 14-131 10-119 (634)
38 cd03564 ANTH_AP180_CALM ANTH d 86.9 4.6 0.0001 37.4 9.1 56 283-338 13-70 (117)
39 PF12348 CLASP_N: CLASP N term 86.2 3.7 8.1E-05 41.1 8.7 69 52-131 133-206 (228)
40 KOG1087 Cytosolic sorting prot 84.1 6 0.00013 45.6 10.0 107 270-383 3-116 (470)
41 cd06224 REM Guanine nucleotide 80.1 3.9 8.4E-05 37.0 5.5 69 15-86 4-86 (122)
42 PF02985 HEAT: HEAT repeat; I 79.5 3.7 7.9E-05 29.5 4.1 29 306-334 1-29 (31)
43 KOG2374 Uncharacterized conser 79.5 20 0.00042 41.8 11.7 111 15-127 10-121 (661)
44 KOG2374 Uncharacterized conser 79.1 17 0.00036 42.3 11.0 105 268-379 7-125 (661)
45 PF13646 HEAT_2: HEAT repeats; 78.5 15 0.00032 30.9 8.2 73 288-374 14-87 (88)
46 PF13646 HEAT_2: HEAT repeats; 76.5 7.5 0.00016 32.7 5.9 60 307-380 1-61 (88)
47 PF12830 Nipped-B_C: Sister ch 74.4 14 0.0003 37.0 8.1 60 315-382 18-77 (187)
48 smart00582 RPR domain present 73.5 18 0.00039 33.1 8.0 94 286-379 11-107 (121)
49 cd03562 CID CID (CTD-Interacti 73.2 25 0.00055 32.0 8.9 98 16-128 7-105 (114)
50 PF13513 HEAT_EZ: HEAT-like re 73.2 8.9 0.00019 30.2 5.2 55 319-377 1-55 (55)
51 PF00618 RasGEF_N: RasGEF N-te 73.0 10 0.00022 33.8 6.0 73 15-90 9-96 (104)
52 PF11467 LEDGF: Lens epitheliu 70.4 12 0.00026 35.1 6.0 69 50-131 6-80 (106)
53 smart00229 RasGEFN Guanine nuc 69.2 21 0.00045 32.8 7.4 82 15-99 12-107 (127)
54 PF12717 Cnd1: non-SMC mitotic 68.6 22 0.00048 35.0 7.9 71 304-381 24-94 (178)
55 PF14500 MMS19_N: Dos2-interac 67.5 26 0.00056 37.3 8.7 67 23-89 181-248 (262)
56 KOG0251 Clathrin assembly prot 65.1 16 0.00034 42.5 6.9 68 268-339 24-95 (491)
57 PF08167 RIX1: rRNA processing 64.9 64 0.0014 31.7 10.3 93 272-379 4-97 (165)
58 COG5098 Chromosome condensatio 63.1 25 0.00054 42.6 8.0 37 46-82 342-378 (1128)
59 KOG1086 Cytosolic sorting prot 62.5 38 0.00081 39.1 9.0 106 17-132 13-121 (594)
60 PF12755 Vac14_Fab1_bd: Vacuol 61.2 52 0.0011 30.0 8.3 73 46-129 23-95 (97)
61 PRK09687 putative lyase; Provi 61.0 29 0.00063 37.1 7.7 74 290-381 12-85 (280)
62 PF12243 CTK3: CTD kinase subu 60.5 70 0.0015 31.4 9.5 95 284-379 17-119 (139)
63 PF07923 N1221: N1221-like pro 60.1 18 0.00039 38.8 5.9 52 50-101 60-117 (293)
64 cd00020 ARM Armadillo/beta-cat 59.2 43 0.00094 28.9 7.2 71 306-380 8-79 (120)
65 KOG1086 Cytosolic sorting prot 57.3 53 0.0012 37.9 9.0 89 289-379 27-123 (594)
66 cd00020 ARM Armadillo/beta-cat 55.8 53 0.0012 28.3 7.2 69 305-378 49-119 (120)
67 COG5098 Chromosome condensatio 55.7 32 0.00069 41.8 7.3 77 304-385 345-421 (1128)
68 KOG3091 Nuclear pore complex, 55.5 73 0.0016 37.2 9.9 115 10-131 313-429 (508)
69 PF02985 HEAT: HEAT repeat; I 55.3 16 0.00034 26.2 3.1 30 51-80 1-30 (31)
70 PF08167 RIX1: rRNA processing 54.2 53 0.0012 32.3 7.7 72 46-131 21-97 (165)
71 PF07651 ANTH: ANTH domain; I 52.5 51 0.0011 34.4 7.7 68 268-338 4-73 (280)
72 KOG2956 CLIP-associating prote 51.8 71 0.0015 37.3 9.0 91 32-132 307-402 (516)
73 KOG2199 Signal transducing ada 50.4 78 0.0017 36.2 8.9 94 287-383 22-122 (462)
74 COG0735 Fur Fe2+/Zn2+ uptake r 49.7 53 0.0011 31.9 6.7 61 273-333 8-69 (145)
75 COG4396 Mu-like prophage host- 47.2 54 0.0012 32.6 6.2 66 284-357 13-83 (170)
76 PF10274 ParcG: Parkin co-regu 46.5 1.8E+02 0.0038 30.0 10.1 114 13-131 39-164 (183)
77 KOG0414 Chromosome condensatio 45.3 45 0.00097 42.4 6.6 36 50-85 359-394 (1251)
78 KOG2025 Chromosome condensatio 43.7 34 0.00074 41.5 5.2 41 45-85 121-162 (892)
79 PF04003 Utp12: Dip2/Utp12 Fam 43.2 1.9E+02 0.0042 25.9 9.0 45 34-79 16-61 (110)
80 KOG2160 Armadillo/beta-catenin 42.8 1.4E+02 0.0031 33.4 9.5 59 315-377 177-238 (342)
81 PF06371 Drf_GBD: Diaphanous G 42.5 89 0.0019 30.2 7.2 55 66-130 132-186 (187)
82 smart00582 RPR domain present 41.7 1.6E+02 0.0035 26.9 8.3 88 29-128 12-104 (121)
83 PRK13800 putative oxidoreducta 40.9 61 0.0013 40.1 7.0 21 355-375 875-895 (897)
84 PTZ00429 beta-adaptin; Provisi 39.2 8.4E+02 0.018 30.2 18.6 72 302-380 475-547 (746)
85 PF01431 Peptidase_M13: Peptid 39.1 8.4 0.00018 38.4 -0.5 28 600-627 13-43 (206)
86 KOG0915 Uncharacterized conser 38.5 78 0.0017 41.5 7.3 105 305-414 1039-1143(1702)
87 PRK09687 putative lyase; Provi 38.2 95 0.0021 33.2 7.1 26 51-76 24-49 (280)
88 KOG0980 Actin-binding protein 36.6 1E+02 0.0022 38.5 7.5 110 13-129 7-117 (980)
89 PF11841 DUF3361: Domain of un 35.3 78 0.0017 31.9 5.5 46 304-349 101-146 (160)
90 KOG4380 Carnitine deficiency a 35.2 51 0.0011 34.3 4.2 76 304-384 135-214 (244)
91 PRK09462 fur ferric uptake reg 34.4 95 0.0021 29.8 5.8 56 277-332 8-65 (148)
92 PRK13800 putative oxidoreducta 34.1 73 0.0016 39.4 6.2 59 306-378 808-866 (897)
93 PF13513 HEAT_EZ: HEAT-like re 33.6 17 0.00038 28.6 0.6 29 47-75 25-53 (55)
94 PF12169 DNA_pol3_gamma3: DNA 33.1 2.2E+02 0.0048 26.5 8.0 66 34-107 4-69 (143)
95 PTZ00429 beta-adaptin; Provisi 32.5 1.9E+02 0.004 35.7 9.1 85 30-132 463-547 (746)
96 PF12830 Nipped-B_C: Sister ch 29.9 1.7E+02 0.0036 29.4 6.9 69 48-133 6-76 (187)
97 PF14676 FANCI_S2: FANCI solen 29.8 1.5E+02 0.0032 29.6 6.4 66 35-104 40-105 (158)
98 KOG2259 Uncharacterized conser 28.7 1.2E+02 0.0026 36.9 6.4 78 37-131 398-475 (823)
99 PF12765 Cohesin_HEAT: HEAT re 28.2 53 0.0011 25.6 2.4 26 49-74 17-42 (42)
100 PF08620 RPAP1_C: RPAP1-like, 27.6 85 0.0019 27.8 3.8 22 24-45 32-53 (73)
101 PRK11639 zinc uptake transcrip 24.5 1.4E+02 0.0031 29.6 5.3 57 275-331 15-72 (169)
102 PF01602 Adaptin_N: Adaptin N 24.2 1.5E+02 0.0033 33.2 6.1 66 19-87 86-151 (526)
103 PF05598 DUF772: Transposase d 23.6 1.9E+02 0.004 24.4 5.1 64 64-132 7-75 (77)
104 PF14225 MOR2-PAG1_C: Cell mor 23.3 1.3E+02 0.0028 32.3 5.0 68 32-103 169-237 (262)
105 PF03224 V-ATPase_H_N: V-ATPas 23.2 3.2E+02 0.0069 29.3 8.0 45 297-341 97-141 (312)
106 PF08389 Xpo1: Exportin 1-like 22.9 1.7E+02 0.0036 26.8 5.1 65 48-126 80-148 (148)
107 cd08330 CARD_ASC_NALP1 Caspase 22.5 1.5E+02 0.0032 26.3 4.4 51 48-98 17-80 (82)
108 PF14663 RasGEF_N_2: Rapamycin 22.2 1.5E+02 0.0033 27.7 4.7 33 49-81 7-39 (115)
109 KOG2011 Sister chromatid cohes 22.1 2.6E+02 0.0057 35.7 7.9 48 33-80 308-356 (1048)
110 KOG1078 Vesicle coat complex C 22.0 3.3E+02 0.0072 33.9 8.4 106 270-384 208-316 (865)
111 KOG1242 Protein containing ada 21.9 3.5E+02 0.0077 32.4 8.5 113 268-384 213-329 (569)
112 PF07814 WAPL: Wings apart-lik 21.9 2.2E+02 0.0047 31.6 6.6 59 48-107 19-77 (361)
113 KOG1967 DNA repair/transcripti 21.5 2.8E+02 0.0061 35.1 7.8 78 20-98 225-304 (1030)
114 PF03700 Sorting_nexin: Sortin 21.4 1.4E+02 0.0031 29.1 4.4 60 475-544 22-90 (129)
115 PF08252 Leader_CPA1: arg-2/CP 21.3 21 0.00045 25.2 -0.8 7 690-696 12-18 (24)
116 PF12031 DUF3518: Domain of un 21.2 4.6E+02 0.01 28.5 8.5 96 7-103 110-225 (257)
117 PF06878 Pkip-1: Pkip-1 protei 20.2 1.9E+02 0.0041 29.4 5.1 36 43-79 115-158 (163)
118 KOG2023 Nuclear transport rece 20.0 1.2E+02 0.0026 37.0 4.2 61 304-368 392-452 (885)
No 1
>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=100.00 E-value=4.4e-45 Score=338.65 Aligned_cols=121 Identities=48% Similarity=0.692 Sum_probs=117.5
Q ss_pred HHHhhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHHHHHH
Q 005358 12 WRSRMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREMQR 91 (700)
Q Consensus 12 ~~~~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrr 91 (700)
|++++|++|||||+||||||+|+|||++|+++.. .|++|||||++||++++||||+||||||||||++|+++|++|+|+
T Consensus 1 ~~~~ll~~ATsdd~~p~pgy~~~Eia~~t~~s~~-~~~ei~d~L~kRL~~~~~hVK~K~Lrilk~l~~~G~~~f~~~~~~ 79 (122)
T cd03572 1 MRRSLLSKATSDDDEPTPGYLYEEIAKLTRKSVG-SCQELLEYLLKRLKRSSPHVKLKVLKIIKHLCEKGNSDFKRELQR 79 (122)
T ss_pred CcHHHHHHHhcCCCCCCchHHHHHHHHHHHcCHH-HHHHHHHHHHHHhcCCCCcchHHHHHHHHHHHhhCCHHHHHHHHH
Confidence 5789999999999999999999999999999875 579999999999999999999999999999999999999999999
Q ss_pred hHHHHHHhhcccCCCCCCCCchhhHHHHHHHHHHHHHhhcCC
Q 005358 92 HSAVVRQLFHYKGQLDPLKGDALNKAVRDMAHEAISAIFSEE 133 (700)
Q Consensus 92 ns~~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll~aLf~d~ 133 (700)
|+++||+|++|+|+|||++||++|++||++|+||+++||+++
T Consensus 80 ~~~~Ik~~~~f~g~~Dp~~Gd~~~~~VR~~A~El~~~if~~~ 121 (122)
T cd03572 80 NSAQIRECANYKGPPDPLKGDSLNEKVREEAQELIKAIFSYS 121 (122)
T ss_pred hHHHHHHHHHcCCCCCcccCcchhHHHHHHHHHHHHHHhccC
Confidence 999999999999999999999999999999999999999965
No 2
>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=99.94 E-value=4.8e-27 Score=216.81 Aligned_cols=114 Identities=29% Similarity=0.399 Sum_probs=103.2
Q ss_pred hhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhh---ccCCCchHHHHHHHHHHHHhcCChhhHHHHHH
Q 005358 15 RMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRL---EHKSPVVKQKALRLIKYSVGKSGTDFRREMQR 91 (700)
Q Consensus 15 ~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL---~~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrr 91 (700)
.+|++||++|+||||+|+|.|||++||++ ..|.+||++|.+|| +++..++++|||+||+||+.+|+++|+.|+|+
T Consensus 6 ~~v~eAT~~d~~gp~~~~l~eIa~~t~~~--~~~~~I~~~l~kRL~~~~~k~wr~~~KaL~ll~yLl~nG~~~~~~~~~~ 83 (125)
T PF01417_consen 6 LKVREATSNDPWGPPGKLLAEIAQLTYNS--KDCQEIMDVLWKRLSKSDGKNWRHVYKALTLLEYLLKNGSERFVDELRD 83 (125)
T ss_dssp HHHHHHTSSSSSS--HHHHHHHHHHTTSC--HHHHHHHHHHHHHHHSSTSSGHHHHHHHHHHHHHHHHHS-HHHHHHHHH
T ss_pred HHHHHHcCCCCCCcCHHHHHHHHHHHhcc--ccHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHHHHHHCCHHHHHHHHH
Confidence 78999999999999999999999999998 45899999999999 67778899999999999999999999999999
Q ss_pred hHHHHHHhhcccCCCCCCCCchhhHHHHHHHHHHHHHhhcC
Q 005358 92 HSAVVRQLFHYKGQLDPLKGDALNKAVRDMAHEAISAIFSE 132 (700)
Q Consensus 92 ns~~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll~aLf~d 132 (700)
+...|+.|++|+| +|| +|++.+..||++|++++++|+++
T Consensus 84 ~~~~I~~l~~f~~-~d~-~g~d~~~~VR~~A~~i~~lL~d~ 122 (125)
T PF01417_consen 84 HIDIIRELQDFQY-VDP-KGKDQGQNVREKAKEILELLNDD 122 (125)
T ss_dssp THHHHHGGGG----BBT-TSTBHHHHHHHHHHHHHHHHTSH
T ss_pred HHHHHhhcceeec-cCC-CCccHHHHHHHHHHHHHHHhCCc
Confidence 9999999999999 798 99999999999999999999985
No 3
>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=99.89 E-value=3.6e-23 Score=192.84 Aligned_cols=114 Identities=21% Similarity=0.240 Sum_probs=106.1
Q ss_pred hhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccCC---CchHHHHHHHHHHHHhcCChhhHHHHHH
Q 005358 15 RMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKS---PVVKQKALRLIKYSVGKSGTDFRREMQR 91 (700)
Q Consensus 15 ~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks---~hVKlKaLKILkyLc~~Gs~~F~r~lrr 91 (700)
.+|++||++|+|+|++.+|.|||+.||+. ..+.+||++|.+||.++. +|| +|||.||.||+.+|+++|+.|+|+
T Consensus 4 ~~vreATs~d~wGp~~~~m~eIa~~t~~~--~~~~~Im~~l~kRL~~~~k~WR~v-yKaL~lleyLl~nGse~vv~~~r~ 80 (123)
T cd03571 4 LKVREATSNDPWGPSGTLMAEIARATYNY--VEFQEIMSMLWKRLNDKGKNWRHV-YKALTLLEYLLKNGSERVVDDARE 80 (123)
T ss_pred HHHHHHcCCCCCCCCHHHHHHHHHHhCCH--HHHHHHHHHHHHHHHhccccHHHH-HHHHHHHHHHHHhCCHHHHHHHHH
Confidence 68999999999999999999999999987 357899999999999774 677 999999999999999999999999
Q ss_pred hHHHHHHhhcccCCCCCCCCchhhHHHHHHHHHHHHHhhcCC
Q 005358 92 HSAVVRQLFHYKGQLDPLKGDALNKAVRDMAHEAISAIFSEE 133 (700)
Q Consensus 92 ns~~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll~aLf~d~ 133 (700)
|.++|++|+.|++.++ .|.+.+..||++|++++++|-+++
T Consensus 81 ~~~~i~~L~~F~~~d~--~g~d~G~~VR~ka~~i~~Ll~D~~ 120 (123)
T cd03571 81 NLYIIRTLKDFQYIDE--NGKDQGINVREKAKEILELLEDDE 120 (123)
T ss_pred hHHHHHhhccceeeCC--CCCchhHHHHHHHHHHHHHhCCHh
Confidence 9999999999999644 888999999999999999998854
No 4
>KOG2056 consensus Equilibrative nucleoside transporter protein [Nucleotide transport and metabolism]
Probab=99.84 E-value=6.6e-21 Score=201.86 Aligned_cols=116 Identities=22% Similarity=0.221 Sum_probs=108.7
Q ss_pred HhhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccCC---CchHHHHHHHHHHHHhcCChhhHHHHH
Q 005358 14 SRMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKS---PVVKQKALRLIKYSVGKSGTDFRREMQ 90 (700)
Q Consensus 14 ~~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks---~hVKlKaLKILkyLc~~Gs~~F~r~lr 90 (700)
..+|+.||++|+|+|.+.+|.|||+.||+.. .+.+||++|.|||++++ +|| ||||.||.||+.+||+.|+.|+|
T Consensus 23 e~kVrdAT~nd~wGPs~~lm~eIA~~ty~~~--e~~eIm~vi~kRl~d~gknWR~V-yKaLtlleyLl~~GSErv~~~~r 99 (336)
T KOG2056|consen 23 ELKVRDATSNDPWGPSGTLMAEIAQATYNFV--EYQEIMDVLWKRLNDSGKNWRHV-YKALTLLEYLLKNGSERVVDETR 99 (336)
T ss_pred HHHHHhccccccCCCchHHHHHHHHHhcCHH--HHHHHHHHHHHHHhhccchHHHH-HHHHHHHHHHHhcCcHHHHHHHH
Confidence 4799999999999999999999999999984 36899999999999888 889 99999999999999999999999
Q ss_pred HhHHHHHHhhcccCCCCCCCCchhhHHHHHHHHHHHHHhhcCCC
Q 005358 91 RHSAVVRQLFHYKGQLDPLKGDALNKAVRDMAHEAISAIFSEEN 134 (700)
Q Consensus 91 rns~~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll~aLf~d~~ 134 (700)
.|+++|++|+.|++..+ .|.+.+..||++|++|+++|=+++-
T Consensus 100 en~~~I~tL~~Fq~iD~--~G~dqG~nVRkkak~l~~LL~D~er 141 (336)
T KOG2056|consen 100 ENIYTIETLKDFQYIDE--DGKDQGLNVRKKAKELLSLLEDDER 141 (336)
T ss_pred hhhHHHHHHhhceeeCC--CCccchHHHHHHHHHHHHHhccHHH
Confidence 99999999999999855 8888899999999999999999663
No 5
>smart00273 ENTH Epsin N-terminal homology (ENTH) domain.
Probab=99.65 E-value=7.6e-16 Score=142.67 Aligned_cols=115 Identities=18% Similarity=0.202 Sum_probs=106.7
Q ss_pred hhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccC-CCchHHHHHHHHHHHHhcCChhhHHHHHHhH
Q 005358 15 RMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHK-SPVVKQKALRLIKYSVGKSGTDFRREMQRHS 93 (700)
Q Consensus 15 ~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~k-s~hVKlKaLKILkyLc~~Gs~~F~r~lrrns 93 (700)
..|.+||++|+|||....++||+..|+.++. .+.+||..|.+||.+. +..|-+|+|-+|.||+.+|+++|+.+.+++.
T Consensus 5 ~~V~kAT~~~~~~p~~k~~~~I~~~t~~~~~-~~~~i~~~l~~Rl~~~~~w~~v~KsL~llh~ll~~G~~~~~~~~~~~~ 83 (127)
T smart00273 5 VKVRKATNNDEWGPKGKHLREIIQGTHNEKS-SFAEIMAVLWRRLNDTKNWRVVYKALILLHYLLRNGSPRVILEALRNR 83 (127)
T ss_pred HHHHHhcCCCCCCcCHHHHHHHHHHHccCHh-hHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHhcCCHHHHHHHHHhh
Confidence 6899999999999999999999999998864 5789999999999987 5556699999999999999999999999999
Q ss_pred HHHHHhhcccCCCCCCCCchhhHHHHHHHHHHHHHhhcC
Q 005358 94 AVVRQLFHYKGQLDPLKGDALNKAVRDMAHEAISAIFSE 132 (700)
Q Consensus 94 ~~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll~aLf~d 132 (700)
..|++|.+|++. |+ .|.+.+..||..|+.|.++|.+.
T Consensus 84 ~~i~~L~~f~~~-~~-~~~d~g~~VR~ya~~L~~~l~~~ 120 (127)
T smart00273 84 NRILNLSDFQDI-DS-RGKDQGANIRTYAKYLLERLEDD 120 (127)
T ss_pred HHHhhHhhCeec-CC-CCeeCcHHHHHHHHHHHHHHcCH
Confidence 999999999997 66 88999999999999999999873
No 6
>cd00197 VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membra
Probab=99.65 E-value=8.9e-16 Score=139.43 Aligned_cols=113 Identities=32% Similarity=0.454 Sum_probs=101.4
Q ss_pred hhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHHHHHHhHH
Q 005358 15 RMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREMQRHSA 94 (700)
Q Consensus 15 ~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrrns~ 94 (700)
.+|.+||+++.+++...++.||+.++++.. +.+.+++++|.+||+++.++|++|||.+|+||+.+|++.|+++++++..
T Consensus 3 ~~v~~AT~~~~~~p~~~~i~~i~d~~~~~~-~~~~~~~~~l~kRl~~~~~~~~lkaL~lLe~lvkN~g~~f~~~i~~~~~ 81 (115)
T cd00197 3 KTVEKATSNENMGPDWPLIMEICDLINETN-VGPKEAVDAIKKRINNKNPHVVLKALTLLEYCVKNCGERFHQEVASNDF 81 (115)
T ss_pred HHHHHHcCCCCCCCCHHHHHHHHHHHHCCC-ccHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHccHHHHHHHHHhHH
Confidence 689999999999999999999999999875 4679999999999999999999999999999999999999999999987
Q ss_pred HHHHhhcccCCCCCCCCchhhHHHHHHHHHHHHHhhc
Q 005358 95 VVRQLFHYKGQLDPLKGDALNKAVRDMAHEAISAIFS 131 (700)
Q Consensus 95 ~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll~aLf~ 131 (700)
.++-+ .| ...+..|+.++..||+++++|+.+..+
T Consensus 82 ~~~l~-~~--~~~~~~~~~~~~~Vr~k~~~l~~~w~~ 115 (115)
T cd00197 82 AVELL-KF--DKSKLLGDDVSTNVREKAIELVQLWAS 115 (115)
T ss_pred HHHHH-Hh--hccccccCCCChHHHHHHHHHHHHHhC
Confidence 76654 45 345568888999999999999998753
No 7
>KOG2057 consensus Predicted equilibrative nucleoside transporter protein [Nucleotide transport and metabolism]
Probab=99.57 E-value=4.9e-15 Score=155.74 Aligned_cols=129 Identities=19% Similarity=0.202 Sum_probs=111.2
Q ss_pred hhhHHHHHHHH-HhhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccCC----CchHHHHHHHHHHH
Q 005358 3 SSRRAVESYWR-SRMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKS----PVVKQKALRLIKYS 77 (700)
Q Consensus 3 ~~r~~v~~~~~-~~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks----~hVKlKaLKILkyL 77 (700)
+.-++|-+|-. ...||+||++|+|++.|-+|.|||+.||.-.-+.+.++|.+|..|+-+.. ++| ||+|-||.||
T Consensus 13 kandaiMNY~e~e~~VREATNdDPWGPsG~lMgeIaeaTfmry~EdFpelmnmL~qRMLedNK~~WRRV-YKSLiLLaYL 91 (499)
T KOG2057|consen 13 KANDAIMNYPEAEMDVREATNDDPWGPSGPLMGEIAEATFMRYMEDFPELMNMLFQRMLEDNKDAWRRV-YKSLILLAYL 91 (499)
T ss_pred HHhHHHhcchHHHHHHHhhccCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHH-HHHHHHHHHH
Confidence 44566666654 35699999999999999999999999986322345799999999986444 789 9999999999
Q ss_pred HhcCChhhHHHHHHhHHHHHHhhcccCCCCCCCCchhhHHHHHHHHHHHHHhhcCCC
Q 005358 78 VGKSGTDFRREMQRHSAVVRQLFHYKGQLDPLKGDALNKAVRDMAHEAISAIFSEEN 134 (700)
Q Consensus 78 c~~Gs~~F~r~lrrns~~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll~aLf~d~~ 134 (700)
+++|+++|+++.|+|+|-+|.|-+|+.++. ||.+++-.||.+.|||++..-+|+.
T Consensus 92 ikNGSER~VqeAREh~YdLR~LEnYhfiDE--hGKDQGINIR~kVKeilEfanDDd~ 146 (499)
T KOG2057|consen 92 IKNGSERFVQEAREHAYDLRRLENYHFIDE--HGKDQGINIRHKVKEILEFANDDDL 146 (499)
T ss_pred HhcccHHHHHHHHHHHHHHHhhhhccchhh--hCccccccHHHHHHHHHHHhccHHH
Confidence 999999999999999999999999999854 8999888999999999998887653
No 8
>cd03564 ANTH_AP180_CALM ANTH domain family; composed of adaptor protein 180 (AP180), clathrin assembly lymphoid myeloid leukemia protein (CALM) and similar proteins. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. AP180 and CALM play important roles in clathrin-mediated endocytosis. AP180 is a brain-specific clathrin-binding protein which stimulates clathrin assembly during the recycling of synaptic vesicles. The ANTH domain is structurally similar to the VHS domain and is composed of a superhelix of eight alpha helices. ANTH domains bind both inositol phospholipids and proteins, and contribute to the nucleation and formation of clathrin coats on membranes. ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that the ANTH domain is a universal component of the machine
Probab=98.99 E-value=2.2e-09 Score=98.74 Aligned_cols=112 Identities=18% Similarity=0.162 Sum_probs=97.4
Q ss_pred hhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHHHHHHhHH
Q 005358 15 RMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREMQRHSA 94 (700)
Q Consensus 15 ~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrrns~ 94 (700)
..|.|||+.+++||-.=-+++|...|+.++. .+.+++.+|.+||.+++..|-+|+|-+|-+|++.|++.|.++++++..
T Consensus 3 ~aV~kAT~~~~~~pk~k~v~~ii~~t~~~~~-~~~~~~~~l~~Rl~~~~w~v~~K~LillH~llr~G~~~~~~~~~~~~~ 81 (117)
T cd03564 3 KAVKKATSHDEAPPKDKHVRKIIAGTSSSPA-SIPSFASALSRRLLDRNWVVVLKALILLHRLLREGHPSFLQELLSRRG 81 (117)
T ss_pred hHHHhhcCCCCCCCChHHHHHHHHHHcCCCC-CHHHHHHHHHHHHccCcHHHHHHHHHHHHHHHhcCCHHHHHHHHHccC
Confidence 5689999999999999999999999998665 468999999999999888888999999999999999999999999955
Q ss_pred HHHHhhcccCCCCCCCCchhhHHHHHHHHHHHHHh
Q 005358 95 VVRQLFHYKGQLDPLKGDALNKAVRDMAHEAISAI 129 (700)
Q Consensus 95 ~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll~aL 129 (700)
.+ .+..|+...+. .|.+.+..||..|+-|.+.|
T Consensus 82 ~l-~l~~~~~~~~~-~~~~~~~~Vr~Ya~yL~~rl 114 (117)
T cd03564 82 WL-NLSNFLDKSSS-LGYGYSAFIRAYARYLDERL 114 (117)
T ss_pred ee-eccccccCCCC-CchhhhHHHHHHHHHHHHHH
Confidence 55 56677755332 57788999999999988765
No 9
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=98.20 E-value=8.8e-06 Score=76.95 Aligned_cols=109 Identities=27% Similarity=0.304 Sum_probs=84.2
Q ss_pred hhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHHHHHHhHH
Q 005358 15 RMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREMQRHSA 94 (700)
Q Consensus 15 ~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrrns~ 94 (700)
.+|.+||+..-.-+.-.+.-|||.+..... ....+.+..|.|||++++|||-+.||+||+.|+.+....|..++...-
T Consensus 3 ~~i~kATs~~l~~~dw~~~l~icD~i~~~~-~~~k~a~r~l~krl~~~n~~v~l~AL~lLe~~vkNcg~~f~~ev~s~~- 80 (133)
T smart00288 3 RLIDKATSPSLLEEDWELILEICDLINSTP-DGPKDAVRLLKKRLNNKNPHVALLALTLLDACVKNCGSKFHLEVASKE- 80 (133)
T ss_pred hHHHHHcCcCCCCcCHHHHHHHHHHHhCCC-ccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHhHH-
Confidence 589999999888888888899999998885 567899999999999999999999999999999999999999986543
Q ss_pred HHHHhhcccCCCCCCCCchhhHHHHHHHHHHHHHhhc
Q 005358 95 VVRQLFHYKGQLDPLKGDALNKAVRDMAHEAISAIFS 131 (700)
Q Consensus 95 ~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll~aLf~ 131 (700)
++.++...--+ +.... .||+++-+++.....
T Consensus 81 fl~~L~~l~~~--~~~~~----~Vk~kil~li~~W~~ 111 (133)
T smart00288 81 FLNELVKLIKP--KYPLP----LVKKRILELIQEWAD 111 (133)
T ss_pred HHHHHHHHHcC--CCCcH----HHHHHHHHHHHHHHH
Confidence 23333322211 11111 177777777665544
No 10
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=98.10 E-value=2.1e-05 Score=75.80 Aligned_cols=108 Identities=20% Similarity=0.356 Sum_probs=87.5
Q ss_pred hhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHHHHHHhHH
Q 005358 15 RMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREMQRHSA 94 (700)
Q Consensus 15 ~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrrns~ 94 (700)
.+|.+||++.-.-.---+.-|||.+..... ...++.+..|.|||+++.|||-+.||.||+.|+.+....|..++... .
T Consensus 3 ~~iekATse~l~~~dw~~il~icD~I~~~~-~~~k~a~ral~KRl~~~n~~v~l~AL~LLe~~vkNCG~~fh~evask-~ 80 (144)
T cd03568 3 DLVEKATDEKLTSENWGLILDVCDKVKSDE-NGAKDCLKAIMKRLNHKDPNVQLRALTLLDACAENCGKRFHQEVASR-D 80 (144)
T ss_pred HHHHHHcCccCCCcCHHHHHHHHHHHhcCC-ccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHhhH-H
Confidence 579999999877666677889999998874 56799999999999999999999999999999999999999998754 4
Q ss_pred HHHHhhcccCCCCCCCCchhhHHHHHHHHHHHHHhhc
Q 005358 95 VVRQLFHYKGQLDPLKGDALNKAVRDMAHEAISAIFS 131 (700)
Q Consensus 95 ~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll~aLf~ 131 (700)
++.++...--. + ....||+++.+++...-.
T Consensus 81 Fl~eL~kl~~~--~-----~~~~Vk~kil~li~~W~~ 110 (144)
T cd03568 81 FTQELKKLIND--R-----VHPTVKEKLREVVKQWAD 110 (144)
T ss_pred HHHHHHHHhcc--c-----CCHHHHHHHHHHHHHHHH
Confidence 55555444322 1 345688888888887744
No 11
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=98.05 E-value=3.2e-05 Score=72.89 Aligned_cols=107 Identities=24% Similarity=0.247 Sum_probs=84.8
Q ss_pred hhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHHHHHHhHH
Q 005358 15 RMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREMQRHSA 94 (700)
Q Consensus 15 ~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrrns~ 94 (700)
.+|.+||+....-.---+.-||+.+..... ....+.+..|.|||++++|||.+.||.||+.|+.++...|..++...--
T Consensus 3 ~~I~kATs~~~~~~D~~~il~icd~I~~~~-~~~k~a~raL~krl~~~n~~vql~AL~lLd~~vkNcg~~f~~~i~s~~f 81 (133)
T cd03561 3 SLIERATSPSLEEPDWALNLELCDLINLKP-NGPKEAARAIRKKIKYGNPHVQLLALTLLELLVKNCGKPFHLQVADKEF 81 (133)
T ss_pred HHHHHHcCcccCCccHHHHHHHHHHHhCCC-CCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCChHHHHHHhhHHH
Confidence 579999998665555567889999998875 4678999999999999999999999999999999999999998887442
Q ss_pred ---HHHHhhcccCCCCCCCCchhhHHHHHHHHHHHHHhhc
Q 005358 95 ---VVRQLFHYKGQLDPLKGDALNKAVRDMAHEAISAIFS 131 (700)
Q Consensus 95 ---~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll~aLf~ 131 (700)
+++-+..- ......||.++-+++.....
T Consensus 82 l~~l~~l~~~~---------~~~~~~Vk~kil~ll~~W~~ 112 (133)
T cd03561 82 LLELVKIAKNS---------PKYDPKVREKALELILAWSE 112 (133)
T ss_pred HHHHHHHhCCC---------CCCCHHHHHHHHHHHHHHHH
Confidence 34333311 13455688888888876554
No 12
>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM. Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....
Probab=98.05 E-value=2.7e-05 Score=73.90 Aligned_cols=108 Identities=28% Similarity=0.349 Sum_probs=80.2
Q ss_pred hhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHHHHHHhH-
Q 005358 15 RMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREMQRHS- 93 (700)
Q Consensus 15 ~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrrns- 93 (700)
.+|.+||+..-.-+---..-+||++....+ ..+.+++..|.|||++..|+|.+-||.||++|+.++++.|++++-+.-
T Consensus 8 ~li~kATs~~~~~~Dw~~~l~icD~i~~~~-~~~kea~~~l~krl~~~~~~vq~~aL~lld~lvkNcg~~f~~ev~~~~f 86 (140)
T PF00790_consen 8 ELIEKATSESLPSPDWSLILEICDLINSSP-DGAKEAARALRKRLKHGNPNVQLLALTLLDALVKNCGPRFHREVASKEF 86 (140)
T ss_dssp HHHHHHT-TTSSS--HHHHHHHHHHHHTST-THHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHSHHHHHHHHTSHHH
T ss_pred HHHHHHhCcCCCCCCHHHHHHHHHHHHcCC-ccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHcCCHHHHHHHhHHHH
Confidence 789999998765555556678999998885 567999999999999999999999999999999999999999986553
Q ss_pred -HHHHHhhcccCCCCCCCCchhhHHHHHHHHHHHHHhh
Q 005358 94 -AVVRQLFHYKGQLDPLKGDALNKAVRDMAHEAISAIF 130 (700)
Q Consensus 94 -~~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll~aLf 130 (700)
..++.+..-+.. .....||+++.+++...-
T Consensus 87 l~~l~~l~~~~~~-------~~~~~Vk~k~l~ll~~W~ 117 (140)
T PF00790_consen 87 LDELVKLIKSKKT-------DPETPVKEKILELLQEWA 117 (140)
T ss_dssp HHHHHHHHHHTTT-------HHHSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHccCCC-------CchhHHHHHHHHHHHHHH
Confidence 233333322221 111228888887776543
No 13
>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=98.03 E-value=5e-05 Score=70.66 Aligned_cols=106 Identities=19% Similarity=0.282 Sum_probs=82.7
Q ss_pred HHHHHHHHhhcCCcccCCCHHHHHHHHHHHhh-cCHHHHHHHHHHHh---CCchHHHHHHHHHHHHHHHhccCchhHHHH
Q 005358 269 EEKLLETIVTYGGVRLQPTRDAIQVFLVEAAK-LDALAMSRALEAKL---QSPLWQVRMKAICVLESILRKKDDEKFSII 344 (700)
Q Consensus 269 E~~LVe~i~T~gGvr~~PSreeLq~Fl~~c~~-Ld~e~V~elL~~kL---~~~~WQvrlRALcvIEaLl~s~~~d~~~~v 344 (700)
-..+|++ +|.... .-|+...+..-.+.+-. -+|..|.+.|..+| ....|.+.+|||.+||.|++.+.. .+
T Consensus 4 ~e~~v~e-AT~~d~-~gp~~~~l~eIa~~t~~~~~~~~I~~~l~kRL~~~~~k~wr~~~KaL~ll~yLl~nG~~----~~ 77 (125)
T PF01417_consen 4 LELKVRE-ATSNDP-WGPPGKLLAEIAQLTYNSKDCQEIMDVLWKRLSKSDGKNWRHVYKALTLLEYLLKNGSE----RF 77 (125)
T ss_dssp HHHHHHH-HTSSSS-SS--HHHHHHHHHHTTSCHHHHHHHHHHHHHHHSSTSSGHHHHHHHHHHHHHHHHHS-H----HH
T ss_pred HHHHHHH-HcCCCC-CCcCHHHHHHHHHHHhccccHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHHHHHHCCH----HH
Confidence 3456777 565443 47888889888888866 67899999999999 789999999999999999998864 45
Q ss_pred HHHHHhhhHHHhhhhcCCC---------hhHHHHHHHHHHHhccc
Q 005358 345 LSYFCENNDVVVKCSESPQ---------SSLREKANKVLSLLGEE 380 (700)
Q Consensus 345 ~~Yf~eN~~~L~r~~~s~q---------~~LReKA~KVL~lLg~~ 380 (700)
...++.+...|+.|..-.- ..||+||++|+.+|.-+
T Consensus 78 ~~~~~~~~~~I~~l~~f~~~d~~g~d~~~~VR~~A~~i~~lL~d~ 122 (125)
T PF01417_consen 78 VDELRDHIDIIRELQDFQYVDPKGKDQGQNVREKAKEILELLNDD 122 (125)
T ss_dssp HHHHHHTHHHHHGGGG---BBTTSTBHHHHHHHHHHHHHHHHTSH
T ss_pred HHHHHHHHHHHhhcceeeccCCCCccHHHHHHHHHHHHHHHhCCc
Confidence 6777888888888876521 24999999999999754
No 14
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=97.99 E-value=5.4e-05 Score=72.70 Aligned_cols=110 Identities=11% Similarity=0.193 Sum_probs=88.8
Q ss_pred hhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHHHHHHhH-
Q 005358 15 RMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREMQRHS- 93 (700)
Q Consensus 15 ~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrrns- 93 (700)
.+|.+||+..-.-+---+.-|||.+....+ ....+.+..|.+||++++|||-+-||.||+.|+.+....|..++.+.-
T Consensus 4 ~~iekAT~~~l~~~dw~~ileicD~In~~~-~~~k~a~rai~krl~~~n~~v~l~AL~LLe~~vkNCG~~fh~evas~~F 82 (139)
T cd03567 4 AWLNKATNPSNREEDWEAIQAFCEQINKEP-EGPQLAVRLLAHKIQSPQEKEALQALTVLEACMKNCGERFHSEVGKFRF 82 (139)
T ss_pred HHHHHHcCccCCCCCHHHHHHHHHHHHcCC-ccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCHHHHHHHHhHHH
Confidence 579999999987777778889999998776 467899999999999999999999999999999999999999887654
Q ss_pred --HHHHHhhcccCCCCCCCCchhhHHHHHHHHHHHHHhhc
Q 005358 94 --AVVRQLFHYKGQLDPLKGDALNKAVRDMAHEAISAIFS 131 (700)
Q Consensus 94 --~~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll~aLf~ 131 (700)
..+|-+. +.+.|......||++.-+++..--.
T Consensus 83 l~el~kl~~------~k~~~~~~~~~Vk~kil~li~~W~~ 116 (139)
T cd03567 83 LNELIKLVS------PKYLGSRTSEKVKTKIIELLYSWTL 116 (139)
T ss_pred HHHHHHHhc------cccCCCCCCHHHHHHHHHHHHHHHH
Confidence 2444442 1223555667899988888776543
No 15
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=97.81 E-value=0.00016 Score=69.44 Aligned_cols=108 Identities=30% Similarity=0.334 Sum_probs=84.8
Q ss_pred hhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHHHHHHhHH
Q 005358 15 RMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREMQRHSA 94 (700)
Q Consensus 15 ~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrrns~ 94 (700)
.+|.+||++...-+--.+.-|||.+...... ...+.+..|.|||++++|||-+-||.||+.|+.+....|..++...-
T Consensus 7 ~~I~kATs~~l~~~dw~~ileicD~In~~~~-~~k~a~ral~krl~~~n~~vql~AL~LLe~~vkNCG~~fh~evas~~- 84 (142)
T cd03569 7 ELIEKATSELLGEPDLASILEICDMIRSKDV-QPKYAMRALKKRLLSKNPNVQLYALLLLESCVKNCGTHFHDEVASRE- 84 (142)
T ss_pred HHHHHHcCcccCccCHHHHHHHHHHHhCCCC-CHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHCCHHHHHHHhhHH-
Confidence 7899999998877777888999999987754 57899999999999999999999999999999999999998887543
Q ss_pred HHHHhhcccCCCCCCCCchhhHHHHHHHHHHHHHhhc
Q 005358 95 VVRQLFHYKGQLDPLKGDALNKAVRDMAHEAISAIFS 131 (700)
Q Consensus 95 ~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll~aLf~ 131 (700)
++.++...--. .....||+++-+++.....
T Consensus 85 fl~~l~~l~~~-------~~~~~Vk~kil~li~~W~~ 114 (142)
T cd03569 85 FMDELKDLIKT-------TKNEEVRQKILELIQAWAL 114 (142)
T ss_pred HHHHHHHHHcc-------cCCHHHHHHHHHHHHHHHH
Confidence 22332221111 2345688888888776654
No 16
>cd00197 VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membra
Probab=97.77 E-value=0.00056 Score=62.43 Aligned_cols=101 Identities=18% Similarity=0.180 Sum_probs=74.2
Q ss_pred HHHHHHhhcCCcccCCCHHHHHHHHHHHhh--cCHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHHHHHH
Q 005358 271 KLLETIVTYGGVRLQPTRDAIQVFLVEAAK--LDALAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSIILSYF 348 (700)
Q Consensus 271 ~LVe~i~T~gGvr~~PSreeLq~Fl~~c~~--Ld~e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~Yf 348 (700)
++|++ +|. ---..|....+..++..... -.+..+..+|..||.++.|.+++|||.+||+|++..+... ..++
T Consensus 3 ~~v~~-AT~-~~~~~p~~~~i~~i~d~~~~~~~~~~~~~~~l~kRl~~~~~~~~lkaL~lLe~lvkN~g~~f----~~~i 76 (115)
T cd00197 3 KTVEK-ATS-NENMGPDWPLIMEICDLINETNVGPKEAVDAIKKRINNKNPHVVLKALTLLEYCVKNCGERF----HQEV 76 (115)
T ss_pred HHHHH-HcC-CCCCCCCHHHHHHHHHHHHCCCccHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHccHHH----HHHH
Confidence 45666 443 23357888888888887766 3568999999999999999999999999999999987543 3455
Q ss_pred HhhhHHHhhh--------hcCCChhHHHHHHHHHHHh
Q 005358 349 CENNDVVVKC--------SESPQSSLREKANKVLSLL 377 (700)
Q Consensus 349 ~eN~~~L~r~--------~~s~q~~LReKA~KVL~lL 377 (700)
+.+.-..+.+ .......||+|+..++..|
T Consensus 77 ~~~~~~~~l~~~~~~~~~~~~~~~~Vr~k~~~l~~~w 113 (115)
T cd00197 77 ASNDFAVELLKFDKSKLLGDDVSTNVREKAIELVQLW 113 (115)
T ss_pred HHhHHHHHHHHhhccccccCCCChHHHHHHHHHHHHH
Confidence 5554222221 2344678999999998876
No 17
>cd03571 ENTH_epsin ENTH domain, Epsin family; The epsin (Eps15 interactor) N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. ENTH and ANTH (E/ANTH) domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. E/ANTH domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that E/ANTH domains are univ
Probab=97.71 E-value=0.00051 Score=64.91 Aligned_cols=105 Identities=18% Similarity=0.253 Sum_probs=83.2
Q ss_pred HHHHHHhhcCCcccCCCHHHHHHHHHHHhhc-CHHHHHHHHHHHhCC--chHHHHHHHHHHHHHHHhccCchhHHHHHHH
Q 005358 271 KLLETIVTYGGVRLQPTRDAIQVFLVEAAKL-DALAMSRALEAKLQS--PLWQVRMKAICVLESILRKKDDEKFSIILSY 347 (700)
Q Consensus 271 ~LVe~i~T~gGvr~~PSreeLq~Fl~~c~~L-d~e~V~elL~~kL~~--~~WQvrlRALcvIEaLl~s~~~d~~~~v~~Y 347 (700)
..|++ +|..-. .-|+...+.+-.+.+-.- ++..|...|.++|.+ ..|..-+|||.+||.|++.+.. .|...
T Consensus 4 ~~vre-ATs~d~-wGp~~~~m~eIa~~t~~~~~~~~Im~~l~kRL~~~~k~WR~vyKaL~lleyLl~nGse----~vv~~ 77 (123)
T cd03571 4 LKVRE-ATSNDP-WGPSGTLMAEIARATYNYVEFQEIMSMLWKRLNDKGKNWRHVYKALTLLEYLLKNGSE----RVVDD 77 (123)
T ss_pred HHHHH-HcCCCC-CCCCHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHhCCH----HHHHH
Confidence 34666 565333 778888888888887663 568999999999954 5999999999999999998863 66888
Q ss_pred HHhhhHHHhhhhcC---------CChhHHHHHHHHHHHhcccc
Q 005358 348 FCENNDVVVKCSES---------PQSSLREKANKVLSLLGEEQ 381 (700)
Q Consensus 348 f~eN~~~L~r~~~s---------~q~~LReKA~KVL~lLg~~~ 381 (700)
|++|...|+.|.+- .-..||+||++|+.||.-+.
T Consensus 78 ~r~~~~~i~~L~~F~~~d~~g~d~G~~VR~ka~~i~~Ll~D~~ 120 (123)
T cd03571 78 ARENLYIIRTLKDFQYIDENGKDQGINVREKAKEILELLEDDE 120 (123)
T ss_pred HHHhHHHHHhhccceeeCCCCCchhHHHHHHHHHHHHHhCCHh
Confidence 89999999887521 11579999999999998653
No 18
>cd03565 VHS_Tom1 VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. The VHS domain of the Tom1 protein is essential for the negative regulation of Interleukin-1 and Tumor Necrosis Factor-induced signaling pathways.
Probab=97.64 E-value=0.00035 Score=67.11 Aligned_cols=110 Identities=18% Similarity=0.224 Sum_probs=83.1
Q ss_pred hhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhcc-CCCchHHHHHHHHHHHHhcCChhhHHHHHHhH
Q 005358 15 RMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEH-KSPVVKQKALRLIKYSVGKSGTDFRREMQRHS 93 (700)
Q Consensus 15 ~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~-ks~hVKlKaLKILkyLc~~Gs~~F~r~lrrns 93 (700)
.+|.+||+..-.-.---+.-|||.+..... ...++.+..|.|||++ +.+||-+-||.||+.|+.++...|..++...
T Consensus 4 ~~IekATse~l~~~dw~~ileicD~In~~~-~~~k~a~ralkkRl~~~~n~~v~l~aL~LLe~~vkNCG~~fh~eiask- 81 (141)
T cd03565 4 QLIEKATDGSLQSEDWGLNMEICDIINETE-DGPKDAVRALKKRLNGNKNHKEVMLTLTVLETCVKNCGHRFHVLVAKK- 81 (141)
T ss_pred HHHHHHcCcCCCCcCHHHHHHHHHHHhCCC-CcHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHccHHHHHHHHHH-
Confidence 589999999876666667889999998764 4678999999999984 6899989999999999999999999998766
Q ss_pred HHHHH-hhcccCCCCCCCCchhhHHHHHHHHHHHHHhhc
Q 005358 94 AVVRQ-LFHYKGQLDPLKGDALNKAVRDMAHEAISAIFS 131 (700)
Q Consensus 94 ~~IK~-l~~F~GppDpl~Gd~l~q~VR~~AkEll~aLf~ 131 (700)
.++.+ +...-.+ +.+ +...||++.-+++...-.
T Consensus 82 ~Fl~e~L~~~i~~----~~~-~~~~Vk~kil~li~~W~~ 115 (141)
T cd03565 82 DFIKDVLVKLINP----KNN-PPTIVQEKVLALIQAWAD 115 (141)
T ss_pred HhhhHHHHHHHcc----cCC-CcHHHHHHHHHHHHHHHH
Confidence 44444 3333211 111 234588777777766543
No 19
>PF07651 ANTH: ANTH domain; InterPro: IPR011417 AP180 is an endocytotic accessory protein that has been implicated in the formation of clathrin-coated pits. The domain is involved in phosphatidylinositol 4,5-bisphosphate binding and is a universal adaptor for nucleation of clathrin coats [, ].; GO: 0005543 phospholipid binding; PDB: 1HX8_A 3ZYM_A 1HFA_A 1HG2_A 3ZYL_B 3ZYK_A 1HG5_A 1HF8_A.
Probab=97.49 E-value=0.00025 Score=73.65 Aligned_cols=114 Identities=19% Similarity=0.074 Sum_probs=82.7
Q ss_pred hhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccC-CCchHHHHHHHHHHHHhcCChhhHHHHHHhH
Q 005358 15 RMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHK-SPVVKQKALRLIKYSVGKSGTDFRREMQRHS 93 (700)
Q Consensus 15 ~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~k-s~hVKlKaLKILkyLc~~Gs~~F~r~lrrns 93 (700)
..|.|||+.++.|+--==+++|...|+. .+. +..++..|.+||.+. +..|-+|+|=+|-.|++.|++.|.+++.++.
T Consensus 6 ~av~KAT~~~~~ppk~Khv~~il~~t~~-~~~-~~~~~~~l~~Rl~~~~~w~V~~K~Lil~H~llr~G~~~~~~~~~~~~ 83 (280)
T PF07651_consen 6 KAVIKATSHDEAPPKEKHVREILSATSS-PES-VAFLFWALSRRLPLTRNWIVALKALILLHRLLRDGHPSFLQELLRYN 83 (280)
T ss_dssp HHHHHHT-SSS---HHHHHHHHHHHCST-TS--HHHHHHHHHHHCTSS-SHHHHHHHHHHHHHHHHHS-CHHHHHHHHTT
T ss_pred HHHHHHcCCCCCCCCHHHHHHHHHHhcC-Ccc-HHHHHHHHHHHccccccHHHHHHHHHHHHHHHHcCchHHHHHHHHcc
Confidence 5689999998888877556889888887 444 579999999999987 7889999999999999999999999999998
Q ss_pred HHHHHhhcccCCCC-CCCCchhhHHHHHHHHHHHHHhh
Q 005358 94 AVVRQLFHYKGQLD-PLKGDALNKAVRDMAHEAISAIF 130 (700)
Q Consensus 94 ~~IK~l~~F~GppD-pl~Gd~l~q~VR~~AkEll~aLf 130 (700)
..+..+..+.+.++ ...+.+.+..||.-|+=|-+-+-
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~ir~Y~~yL~~rl~ 121 (280)
T PF07651_consen 84 RRLFDLSNIWDFDDSSSKSWDYSAFIRAYAKYLDERLS 121 (280)
T ss_dssp -----TT---T---SSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred cchhhhccccccccCCccccchhHHHHHHHHHHHHHHH
Confidence 88888888887411 13677888899999988776553
No 20
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=97.28 E-value=0.0016 Score=71.65 Aligned_cols=111 Identities=26% Similarity=0.415 Sum_probs=89.9
Q ss_pred hhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHHHHHHhH-
Q 005358 15 RMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREMQRHS- 93 (700)
Q Consensus 15 ~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrrns- 93 (700)
.+|.|||+.....----+.-+||.+..+++ +..++.+..|+|||+++.|||-+-||.||+-|+.+-...|++++-.+-
T Consensus 11 ~~v~KAT~e~nT~enW~~IlDvCD~v~~~~-~~~kd~lk~i~KRln~~dphV~L~AlTLlda~~~NCg~~~r~EVsSr~F 89 (462)
T KOG2199|consen 11 QDVEKATDEKNTSENWSLILDVCDKVGSDP-DGGKDCLKAIMKRLNHKDPHVVLQALTLLDACVANCGKRFRLEVSSRDF 89 (462)
T ss_pred HHHHHhcCcccccccHHHHHHHHHhhcCCC-cccHHHHHHHHHHhcCCCcchHHHHHHHHHHHHHhcchHHHHHHhhhhH
Confidence 678899987766666667778999988887 678999999999999999999999999999999999999999986543
Q ss_pred -HHHHHhhcccCCCCCCCCchhhHHHHHHHHHHHHHhhcCC
Q 005358 94 -AVVRQLFHYKGQLDPLKGDALNKAVRDMAHEAISAIFSEE 133 (700)
Q Consensus 94 -~~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll~aLf~d~ 133 (700)
..++.+.+=++ ...++.+||..-+|..+ .|-++
T Consensus 90 ~~el~al~~~~~------h~kV~~k~~~lv~eWse-e~K~D 123 (462)
T KOG2199|consen 90 TTELRALIESKA------HPKVCEKMRDLVKEWSE-EFKKD 123 (462)
T ss_pred HHHHHHHHhhcc------cHHHHHHHHHHHHHHHH-HhccC
Confidence 34454443222 24789999999999998 67644
No 21
>KOG2056 consensus Equilibrative nucleoside transporter protein [Nucleotide transport and metabolism]
Probab=97.24 E-value=0.0012 Score=71.64 Aligned_cols=96 Identities=19% Similarity=0.250 Sum_probs=74.7
Q ss_pred CCCHHHHHHHHHHHhh-cCHHHHHHHHHHHh--CCchHHHHHHHHHHHHHHHhccCchhHHHHHHHHHhhhHHHhhhhcC
Q 005358 285 QPTRDAIQVFLVEAAK-LDALAMSRALEAKL--QSPLWQVRMKAICVLESILRKKDDEKFSIILSYFCENNDVVVKCSES 361 (700)
Q Consensus 285 ~PSreeLq~Fl~~c~~-Ld~e~V~elL~~kL--~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~Yf~eN~~~L~r~~~s 361 (700)
-|+...|.+....--. -++..|+..|..|| ....|...+|||.+||.||+-+. +.|...+++|...|..|.+-
T Consensus 36 GPs~~lm~eIA~~ty~~~e~~eIm~vi~kRl~d~gknWR~VyKaLtlleyLl~~GS----Erv~~~~ren~~~I~tL~~F 111 (336)
T KOG2056|consen 36 GPSGTLMAEIAQATYNFVEYQEIMDVLWKRLNDSGKNWRHVYKALTLLEYLLKNGS----ERVVDETRENIYTIETLKDF 111 (336)
T ss_pred CCchHHHHHHHHHhcCHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHhcCc----HHHHHHHHhhhHHHHHHhhc
Confidence 5566666555444322 55689999999999 47999999999999999999665 36788999999888887654
Q ss_pred CCh---------hHHHHHHHHHHHhcccccCC
Q 005358 362 PQS---------SLREKANKVLSLLGEEQAGG 384 (700)
Q Consensus 362 ~q~---------~LReKA~KVL~lLg~~~~~~ 384 (700)
... -||+||++||.||.-++...
T Consensus 112 q~iD~~G~dqG~nVRkkak~l~~LL~D~erLk 143 (336)
T KOG2056|consen 112 QYIDEDGKDQGLNVRKKAKELLSLLEDDERLK 143 (336)
T ss_pred eeeCCCCccchHHHHHHHHHHHHHhccHHHHH
Confidence 332 38999999999999876554
No 22
>KOG1087 consensus Cytosolic sorting protein GGA2/TOM1 [Intracellular trafficking, secretion, and vesicular transport]
Probab=97.12 E-value=0.0027 Score=71.89 Aligned_cols=109 Identities=26% Similarity=0.250 Sum_probs=86.8
Q ss_pred hhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHHHHHHhHH
Q 005358 15 RMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREMQRHSA 94 (700)
Q Consensus 15 ~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrrns~ 94 (700)
++|.+||+..-..+---+--|||.+.-.... ...|++..|.|||+++.+||.+=||.||.-|+.+-...|...+.+.=-
T Consensus 4 ~~IdkAT~~~l~~pDWa~NleIcD~IN~~~~-~~~eAvralkKRi~~k~s~vq~lALtlLE~cvkNCG~~fh~~Va~k~f 82 (470)
T KOG1087|consen 4 KLIDKATSESLAEPDWALNLEICDLINSTEG-GPKEAVRALKKRLNSKNSKVQLLALTLLETCVKNCGYSFHLQVASKEF 82 (470)
T ss_pred HHHHHhhcccccCccHHHHHHHHHHHhcCcc-CcHHHHHHHHHHhccCCcHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence 6899999998777777788899999987754 578999999999999999999999999999999999999866555432
Q ss_pred HHHHhhcccCCCCCCCCchhhHHHHHHHHHHHHHhhc
Q 005358 95 VVRQLFHYKGQLDPLKGDALNKAVRDMAHEAISAIFS 131 (700)
Q Consensus 95 ~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll~aLf~ 131 (700)
+=...+-|+.. + ...+||+++=+||+.=..
T Consensus 83 L~emVk~~k~~-----~--~~~~Vr~kiL~LI~~W~~ 112 (470)
T KOG1087|consen 83 LNEMVKRPKNK-----P--RDLKVREKILELIDTWQQ 112 (470)
T ss_pred HHHHHhccccC-----C--cchhHHHHHHHHHHHHHH
Confidence 22233444432 2 567799999888887655
No 23
>KOG0251 consensus Clathrin assembly protein AP180 and related proteins, contain ENTH domain [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=96.74 E-value=0.0068 Score=69.10 Aligned_cols=114 Identities=21% Similarity=0.163 Sum_probs=90.4
Q ss_pred hhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccC-CCchHHHHHHHHHHHHhcCChhhHHHHHHhH
Q 005358 15 RMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHK-SPVVKQKALRLIKYSVGKSGTDFRREMQRHS 93 (700)
Q Consensus 15 ~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~k-s~hVKlKaLKILkyLc~~Gs~~F~r~lrrns 93 (700)
+.|-|||+-|+.|+--=-+++|-.+|..+..+ +..+++-|.+||++. +-.|=+|||=+|-+|+.+|.+.|..++....
T Consensus 26 ~AV~KATsh~~~ppk~k~l~~Il~~ts~~~~~-i~~~v~aLs~Rl~~TrnW~VAlKsLIliH~ll~~G~~~f~~~l~~~~ 104 (491)
T KOG0251|consen 26 KAVVKATSHDDMPPKDKYLDEILSATSSSPAS-IPSCVHALSERLNKTRNWTVALKALILIHRLLKEGDPSFEQELLSRN 104 (491)
T ss_pred HHHHhhccCCCCCccHHHHHHHHHHhcCCccc-HHHHHHHHHHHhCCCcceeehHHHHHHHHHHHhcCcHHHHHHHHhcc
Confidence 77899999997766555567788888887654 589999999999988 7778899999999999999999998887777
Q ss_pred HHHHHhhcccCCCCCCCCchhhHHHHHHHHHHHHHhhc
Q 005358 94 AVVRQLFHYKGQLDPLKGDALNKAVRDMAHEAISAIFS 131 (700)
Q Consensus 94 ~~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll~aLf~ 131 (700)
.+=.|..|+-.-- -.+.+....||.-|+=|=+.+.-
T Consensus 105 -~~l~lS~F~d~s~-~~~~d~safVR~Ya~YLderl~~ 140 (491)
T KOG0251|consen 105 -LILNLSDFRDKSS-SLTWDMSAFVRTYALYLDERLEC 140 (491)
T ss_pred -cccchhhhhcccc-cccchhhHHHHHHHHHHHHHHHH
Confidence 3334566663221 14678899999999877776654
No 24
>smart00273 ENTH Epsin N-terminal homology (ENTH) domain.
Probab=96.68 E-value=0.032 Score=52.11 Aligned_cols=105 Identities=18% Similarity=0.265 Sum_probs=76.1
Q ss_pred HHHHHHHHhhcCCcccCCCHHHHHHHHHHHhhc--CHHHHHHHHHHHhCCc-hHHHHHHHHHHHHHHHhccCchhHHHHH
Q 005358 269 EEKLLETIVTYGGVRLQPTRDAIQVFLVEAAKL--DALAMSRALEAKLQSP-LWQVRMKAICVLESILRKKDDEKFSIIL 345 (700)
Q Consensus 269 E~~LVe~i~T~gGvr~~PSreeLq~Fl~~c~~L--d~e~V~elL~~kL~~~-~WQvrlRALcvIEaLl~s~~~d~~~~v~ 345 (700)
|..+.+ +|..- -.-|+..-++.-+..+..- ++..|...|..+|.+. .|.+-+|+|.+|+.||+.+.. .+.
T Consensus 4 e~~V~k--AT~~~-~~~p~~k~~~~I~~~t~~~~~~~~~i~~~l~~Rl~~~~~w~~v~KsL~llh~ll~~G~~----~~~ 76 (127)
T smart00273 4 EVKVRK--ATNND-EWGPKGKHLREIIQGTHNEKSSFAEIMAVLWRRLNDTKNWRVVYKALILLHYLLRNGSP----RVI 76 (127)
T ss_pred HHHHHH--hcCCC-CCCcCHHHHHHHHHHHccCHhhHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHhcCCH----HHH
Confidence 444444 45433 3677777777777776654 6799999999999665 999999999999999998864 233
Q ss_pred HHHHhhhHHHhhhhcCCC---------hhHHHHHHHHHHHhccc
Q 005358 346 SYFCENNDVVVKCSESPQ---------SSLREKANKVLSLLGEE 380 (700)
Q Consensus 346 ~Yf~eN~~~L~r~~~s~q---------~~LReKA~KVL~lLg~~ 380 (700)
..+..+...+..|..-.. .-||++|..|+.+|...
T Consensus 77 ~~~~~~~~~i~~L~~f~~~~~~~~d~g~~VR~ya~~L~~~l~~~ 120 (127)
T smart00273 77 LEALRNRNRILNLSDFQDIDSRGKDQGANIRTYAKYLLERLEDD 120 (127)
T ss_pred HHHHHhhHHHhhHhhCeecCCCCeeCcHHHHHHHHHHHHHHcCH
Confidence 444556666666554432 25999999999998764
No 25
>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=96.30 E-value=0.023 Score=53.97 Aligned_cols=86 Identities=13% Similarity=0.201 Sum_probs=67.8
Q ss_pred HHHHHHHHHHhhcCHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHHHHHHHhhhHHHhhhhcC-------
Q 005358 289 DAIQVFLVEAAKLDALAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSIILSYFCENNDVVVKCSES------- 361 (700)
Q Consensus 289 eeLq~Fl~~c~~Ld~e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~Yf~eN~~~L~r~~~s------- 361 (700)
+||.....+ +.-.|..|++.|.+||++..--|++|||-+|-+|+..+.. .+..+.++|...|..|.+-
T Consensus 23 ~Eia~~t~~-s~~~~~ei~d~L~kRL~~~~~hVK~K~Lrilk~l~~~G~~----~f~~~~~~~~~~Ik~~~~f~g~~Dp~ 97 (122)
T cd03572 23 EEIAKLTRK-SVGSCQELLEYLLKRLKRSSPHVKLKVLKIIKHLCEKGNS----DFKRELQRNSAQIRECANYKGPPDPL 97 (122)
T ss_pred HHHHHHHHc-CHHHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHHhhCCH----HHHHHHHHhHHHHHHHHHcCCCCCcc
Confidence 455555544 3346789999999999888888999999999999998863 4467889999988888754
Q ss_pred ----CChhHHHHHHHHHHHhcc
Q 005358 362 ----PQSSLREKANKVLSLLGE 379 (700)
Q Consensus 362 ----~q~~LReKA~KVL~lLg~ 379 (700)
+-..||++|+.++.+|-.
T Consensus 98 ~Gd~~~~~VR~~A~El~~~if~ 119 (122)
T cd03572 98 KGDSLNEKVREEAQELIKAIFS 119 (122)
T ss_pred cCcchhHHHHHHHHHHHHHHhc
Confidence 335699999999998743
No 26
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=95.85 E-value=0.073 Score=51.59 Aligned_cols=93 Identities=15% Similarity=0.167 Sum_probs=70.0
Q ss_pred HHHHHHHHHHhhc-----CHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHHHHHHHhhhHHHhhhhcC-C
Q 005358 289 DAIQVFLVEAAKL-----DALAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSIILSYFCENNDVVVKCSES-P 362 (700)
Q Consensus 289 eeLq~Fl~~c~~L-----d~e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~Yf~eN~~~L~r~~~s-~ 362 (700)
+.....+.=|-.+ .+...+.+|..||.+..-.++++||.+||++++..+......|.. ++-.+.|.++... .
T Consensus 16 ~dw~~il~icD~I~~~~~~~k~a~ral~KRl~~~n~~v~l~AL~LLe~~vkNCG~~fh~evas--k~Fl~eL~kl~~~~~ 93 (144)
T cd03568 16 ENWGLILDVCDKVKSDENGAKDCLKAIMKRLNHKDPNVQLRALTLLDACAENCGKRFHQEVAS--RDFTQELKKLINDRV 93 (144)
T ss_pred cCHHHHHHHHHHHhcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHhh--HHHHHHHHHHhcccC
Confidence 3444445444443 346888999999998888999999999999999988765544433 2333567666666 8
Q ss_pred ChhHHHHHHHHHHHhcccccC
Q 005358 363 QSSLREKANKVLSLLGEEQAG 383 (700)
Q Consensus 363 q~~LReKA~KVL~lLg~~~~~ 383 (700)
+..||+|+..++..|......
T Consensus 94 ~~~Vk~kil~li~~W~~~f~~ 114 (144)
T cd03568 94 HPTVKEKLREVVKQWADEFKN 114 (144)
T ss_pred CHHHHHHHHHHHHHHHHHhCC
Confidence 899999999999999877764
No 27
>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM. Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....
Probab=95.54 E-value=0.11 Score=49.53 Aligned_cols=105 Identities=20% Similarity=0.210 Sum_probs=69.5
Q ss_pred HHHHHHHhhcCCcccCCCHHHHHHHHHHHhh-----cCHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHH
Q 005358 270 EKLLETIVTYGGVRLQPTRDAIQVFLVEAAK-----LDALAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSII 344 (700)
Q Consensus 270 ~~LVe~i~T~gGvr~~PSreeLq~Fl~~c~~-----Ld~e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v 344 (700)
..+|+..|.. ....| +...++.=|-. -.+..++.+|..||.+.+-.++++||.++|++++..+......|
T Consensus 7 ~~li~kATs~--~~~~~---Dw~~~l~icD~i~~~~~~~kea~~~l~krl~~~~~~vq~~aL~lld~lvkNcg~~f~~ev 81 (140)
T PF00790_consen 7 TELIEKATSE--SLPSP---DWSLILEICDLINSSPDGAKEAARALRKRLKHGNPNVQLLALTLLDALVKNCGPRFHREV 81 (140)
T ss_dssp HHHHHHHT-T--TSSS-----HHHHHHHHHHHHTSTTHHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHSHHHHHHHH
T ss_pred HHHHHHHhCc--CCCCC---CHHHHHHHHHHHHcCCccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence 4577774443 22333 44444444443 24578999999999999999999999999999998765443222
Q ss_pred HH-HHHhhhHHHhhh-hcCCChh---HHHHHHHHHHHhccccc
Q 005358 345 LS-YFCENNDVVVKC-SESPQSS---LREKANKVLSLLGEEQA 382 (700)
Q Consensus 345 ~~-Yf~eN~~~L~r~-~~s~q~~---LReKA~KVL~lLg~~~~ 382 (700)
.. =|. +.|.++ ....... ||+|+.++|..|+....
T Consensus 82 ~~~~fl---~~l~~l~~~~~~~~~~~Vk~k~l~ll~~W~~~f~ 121 (140)
T PF00790_consen 82 ASKEFL---DELVKLIKSKKTDPETPVKEKILELLQEWAEAFK 121 (140)
T ss_dssp TSHHHH---HHHHHHHHHTTTHHHSHHHHHHHHHHHHHHHHTT
T ss_pred hHHHHH---HHHHHHHccCCCCchhHHHHHHHHHHHHHHHHHC
Confidence 11 122 445553 3344444 89999999999998873
No 28
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=95.46 E-value=0.29 Score=46.32 Aligned_cols=109 Identities=17% Similarity=0.130 Sum_probs=76.7
Q ss_pred HHHHHHhhcCCcccCCCHHHHHHHHHHHhhc--CHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHHHH-H
Q 005358 271 KLLETIVTYGGVRLQPTRDAIQVFLVEAAKL--DALAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSIILS-Y 347 (700)
Q Consensus 271 ~LVe~i~T~gGvr~~PSreeLq~Fl~~c~~L--d~e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~-Y 347 (700)
.+|+..+.+ .-..|--+.+-.+......- .+...+.+|..||++++=.++++||.+||++++..+...+..+.. =
T Consensus 3 ~~I~kATs~--~~~~~D~~~il~icd~I~~~~~~~k~a~raL~krl~~~n~~vql~AL~lLd~~vkNcg~~f~~~i~s~~ 80 (133)
T cd03561 3 SLIERATSP--SLEEPDWALNLELCDLINLKPNGPKEAARAIRKKIKYGNPHVQLLALTLLELLVKNCGKPFHLQVADKE 80 (133)
T ss_pred HHHHHHcCc--ccCCccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCChHHHHHHhhHH
Confidence 355653333 22345555666666665554 678999999999998888999999999999999887654444433 2
Q ss_pred HHhhhHHHhhhhc---CCChhHHHHHHHHHHHhcccccCC
Q 005358 348 FCENNDVVVKCSE---SPQSSLREKANKVLSLLGEEQAGG 384 (700)
Q Consensus 348 f~eN~~~L~r~~~---s~q~~LReKA~KVL~lLg~~~~~~ 384 (700)
|. ..+.++.. .....||+|+..++..|.......
T Consensus 81 fl---~~l~~l~~~~~~~~~~Vk~kil~ll~~W~~~f~~~ 117 (133)
T cd03561 81 FL---LELVKIAKNSPKYDPKVREKALELILAWSESFGGH 117 (133)
T ss_pred HH---HHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHhcCC
Confidence 22 23555443 467889999999999998877664
No 29
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=95.37 E-value=0.38 Score=45.76 Aligned_cols=108 Identities=13% Similarity=0.131 Sum_probs=74.3
Q ss_pred HHHHHHhhcCCcccCCCHHHHHHHHHHHhh--cCHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHHHHH-
Q 005358 271 KLLETIVTYGGVRLQPTRDAIQVFLVEAAK--LDALAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSIILSY- 347 (700)
Q Consensus 271 ~LVe~i~T~gGvr~~PSreeLq~Fl~~c~~--Ld~e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~Y- 347 (700)
.+|+. +|. ..-..|--+.+-.|....+. -.+...+.+|..||.++.-.++++||-++|++++..+......|.+.
T Consensus 3 ~~i~k-ATs-~~l~~~dw~~~l~icD~i~~~~~~~k~a~r~l~krl~~~n~~v~l~AL~lLe~~vkNcg~~f~~ev~s~~ 80 (133)
T smart00288 3 RLIDK-ATS-PSLLEEDWELILEICDLINSTPDGPKDAVRLLKKRLNNKNPHVALLALTLLDACVKNCGSKFHLEVASKE 80 (133)
T ss_pred hHHHH-HcC-cCCCCcCHHHHHHHHHHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHhHH
Confidence 45666 443 22235555556666555544 23678999999999988888999999999999999876655444433
Q ss_pred HHhhhHHHhhhhcCCCh-h-HHHHHHHHHHHhcccccC
Q 005358 348 FCENNDVVVKCSESPQS-S-LREKANKVLSLLGEEQAG 383 (700)
Q Consensus 348 f~eN~~~L~r~~~s~q~-~-LReKA~KVL~lLg~~~~~ 383 (700)
|. +.|.++...... + ||+|+..++..+......
T Consensus 81 fl---~~L~~l~~~~~~~~~Vk~kil~li~~W~~~f~~ 115 (133)
T smart00288 81 FL---NELVKLIKPKYPLPLVKKRILELIQEWADAFKN 115 (133)
T ss_pred HH---HHHHHHHcCCCCcHHHHHHHHHHHHHHHHHHcC
Confidence 44 455554444333 3 899999999988876654
No 30
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=94.74 E-value=0.67 Score=44.89 Aligned_cols=107 Identities=21% Similarity=0.216 Sum_probs=72.2
Q ss_pred HHHHHHhhcCCcccCCCHHHHHHHHHHHhh--cCHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHHHH-H
Q 005358 271 KLLETIVTYGGVRLQPTRDAIQVFLVEAAK--LDALAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSIILS-Y 347 (700)
Q Consensus 271 ~LVe~i~T~gGvr~~PSreeLq~Fl~~c~~--Ld~e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~-Y 347 (700)
.+|+. .|... -..|--+.+-.+...++. -.+...+.+|..||+++.-.++++||.+||++++..+......|.. =
T Consensus 4 ~~iek-AT~~~-l~~~dw~~ileicD~In~~~~~~k~a~rai~krl~~~n~~v~l~AL~LLe~~vkNCG~~fh~evas~~ 81 (139)
T cd03567 4 AWLNK-ATNPS-NREEDWEAIQAFCEQINKEPEGPQLAVRLLAHKIQSPQEKEALQALTVLEACMKNCGERFHSEVGKFR 81 (139)
T ss_pred HHHHH-HcCcc-CCCCCHHHHHHHHHHHHcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCHHHHHHHHhHH
Confidence 34555 34322 234444445555544443 2235678899999999999999999999999999988765544432 2
Q ss_pred HHhhhHHHhhhhc------CCChhHHHHHHHHHHHhccccc
Q 005358 348 FCENNDVVVKCSE------SPQSSLREKANKVLSLLGEEQA 382 (700)
Q Consensus 348 f~eN~~~L~r~~~------s~q~~LReKA~KVL~lLg~~~~ 382 (700)
|. +.+.++.. ..+..||+|.-.++..|.....
T Consensus 82 Fl---~el~kl~~~k~~~~~~~~~Vk~kil~li~~W~~~f~ 119 (139)
T cd03567 82 FL---NELIKLVSPKYLGSRTSEKVKTKIIELLYSWTLELP 119 (139)
T ss_pred HH---HHHHHHhccccCCCCCCHHHHHHHHHHHHHHHHHhc
Confidence 22 34555553 2578899999999999987665
No 31
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=94.71 E-value=0.64 Score=44.95 Aligned_cols=110 Identities=18% Similarity=0.131 Sum_probs=72.9
Q ss_pred HHHHHHhhcCCcccCCCHHHHHHHHHHHhh--cCHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHHHHHH
Q 005358 271 KLLETIVTYGGVRLQPTRDAIQVFLVEAAK--LDALAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSIILSYF 348 (700)
Q Consensus 271 ~LVe~i~T~gGvr~~PSreeLq~Fl~~c~~--Ld~e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~Yf 348 (700)
.+|+. +|. ..-..|--+.+-.+...... -.+...+.+|.+||.++.-.++++||-+||++++..+...+..|.+
T Consensus 7 ~~I~k-ATs-~~l~~~dw~~ileicD~In~~~~~~k~a~ral~krl~~~n~~vql~AL~LLe~~vkNCG~~fh~evas-- 82 (142)
T cd03569 7 ELIEK-ATS-ELLGEPDLASILEICDMIRSKDVQPKYAMRALKKRLLSKNPNVQLYALLLLESCVKNCGTHFHDEVAS-- 82 (142)
T ss_pred HHHHH-HcC-cccCccCHHHHHHHHHHHhCCCCCHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHCCHHHHHHHhh--
Confidence 45666 343 12233333333333333332 4457889999999999999999999999999999877655433333
Q ss_pred HhhhHHHhhhhc-CCChhHHHHHHHHHHHhcccccCC
Q 005358 349 CENNDVVVKCSE-SPQSSLREKANKVLSLLGEEQAGG 384 (700)
Q Consensus 349 ~eN~~~L~r~~~-s~q~~LReKA~KVL~lLg~~~~~~ 384 (700)
++-.+.|.++.. ..+..||+|+-.++..|.......
T Consensus 83 ~~fl~~l~~l~~~~~~~~Vk~kil~li~~W~~~f~~~ 119 (142)
T cd03569 83 REFMDELKDLIKTTKNEEVRQKILELIQAWALAFRNK 119 (142)
T ss_pred HHHHHHHHHHHcccCCHHHHHHHHHHHHHHHHHhCCC
Confidence 222244555443 677889999999999998766543
No 32
>cd03565 VHS_Tom1 VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. The VHS domain of the Tom1 protein is essential for the negative regulation of Interleukin-1 and Tumor Necrosis Factor-induced signaling pathways.
Probab=93.86 E-value=0.6 Score=45.09 Aligned_cols=107 Identities=17% Similarity=0.204 Sum_probs=70.6
Q ss_pred HHHHHHHhhcCCcccCCCHHHHHHHHHHHhhc-----CHHHHHHHHHHHhC-CchHHHHHHHHHHHHHHHhccCchhHHH
Q 005358 270 EKLLETIVTYGGVRLQPTRDAIQVFLVEAAKL-----DALAMSRALEAKLQ-SPLWQVRMKAICVLESILRKKDDEKFSI 343 (700)
Q Consensus 270 ~~LVe~i~T~gGvr~~PSreeLq~Fl~~c~~L-----d~e~V~elL~~kL~-~~~WQvrlRALcvIEaLl~s~~~d~~~~ 343 (700)
..+|+. +|... .+.+..+-.++=|-.+ .+...+.+|.+||. .+.-+++++||.+||++++..+......
T Consensus 3 ~~~Iek-ATse~----l~~~dw~~ileicD~In~~~~~~k~a~ralkkRl~~~~n~~v~l~aL~LLe~~vkNCG~~fh~e 77 (141)
T cd03565 3 GQLIEK-ATDGS----LQSEDWGLNMEICDIINETEDGPKDAVRALKKRLNGNKNHKEVMLTLTVLETCVKNCGHRFHVL 77 (141)
T ss_pred hHHHHH-HcCcC----CCCcCHHHHHHHHHHHhCCCCcHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHccHHHHHH
Confidence 456766 44422 2233555555555443 34688899999997 5678899999999999999888665544
Q ss_pred HHHHHHhhhHH-Hhhhhc---CCChhHHHHHHHHHHHhcccccC
Q 005358 344 ILSYFCENNDV-VVKCSE---SPQSSLREKANKVLSLLGEEQAG 383 (700)
Q Consensus 344 v~~Yf~eN~~~-L~r~~~---s~q~~LReKA~KVL~lLg~~~~~ 383 (700)
|.. ++-.+. |.++.. .++..||+|...++..|......
T Consensus 78 ias--k~Fl~e~L~~~i~~~~~~~~~Vk~kil~li~~W~~~f~~ 119 (141)
T cd03565 78 VAK--KDFIKDVLVKLINPKNNPPTIVQEKVLALIQAWADAFRG 119 (141)
T ss_pred HHH--HHhhhHHHHHHHcccCCCcHHHHHHHHHHHHHHHHHhCC
Confidence 432 122243 455443 24568999999999998876644
No 33
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=90.38 E-value=1.2 Score=43.95 Aligned_cols=82 Identities=17% Similarity=0.282 Sum_probs=60.3
Q ss_pred HHHHHHhccchhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHHHHHHhHHHHHHhhcccCCCCCCCCchhh
Q 005358 36 ICELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREMQRHSAVVRQLFHYKGQLDPLKGDALN 115 (700)
Q Consensus 36 IA~~t~~s~~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrrns~~IK~l~~F~GppDpl~Gd~l~ 115 (700)
++.++...+ ..+...++.|.++|.+++|.|+.-||.+|.||+.++--.++..+- ..+++-+ -|+ +
T Consensus 12 l~DL~~r~~-~~ve~~~~~l~~~L~D~~~~VR~~al~~Ls~Li~~d~ik~k~~l~--~~~l~~l------~D~------~ 76 (178)
T PF12717_consen 12 LGDLCIRYP-NLVEPYLPNLYKCLRDEDPLVRKTALLVLSHLILEDMIKVKGQLF--SRILKLL------VDE------N 76 (178)
T ss_pred HHHHHHhCc-HHHHhHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCceeehhhhh--HHHHHHH------cCC------C
Confidence 445555565 577889999999999999999999999999999876555554431 1223322 243 5
Q ss_pred HHHHHHHHHHHHHhhcC
Q 005358 116 KAVRDMAHEAISAIFSE 132 (700)
Q Consensus 116 q~VR~~AkEll~aLf~d 132 (700)
..||+.|+.++.-+.-.
T Consensus 77 ~~Ir~~A~~~~~e~~~~ 93 (178)
T PF12717_consen 77 PEIRSLARSFFSELLKK 93 (178)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 56999999998888764
No 34
>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=89.59 E-value=1.8 Score=43.37 Aligned_cols=89 Identities=20% Similarity=0.178 Sum_probs=58.2
Q ss_pred HHHHHHHHHHhhcCHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccC--chhHHHHHHHHHhhhHHHhhhhcCCChhH
Q 005358 289 DAIQVFLVEAAKLDALAMSRALEAKLQSPLWQVRMKAICVLESILRKKD--DEKFSIILSYFCENNDVVVKCSESPQSSL 366 (700)
Q Consensus 289 eeLq~Fl~~c~~Ld~e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~--~d~~~~v~~Yf~eN~~~L~r~~~s~q~~L 366 (700)
..|..+++.|. .....+...|..-+.+++|++|..++-.+..++.+-. .+..+ ...++..-...|.+|...+.+.|
T Consensus 116 ~~L~~i~~~~~-~~~~~~~~~l~~~~~~Kn~~vR~~~~~~l~~~l~~~~~~~~~l~-~~~~~~~l~~~l~~~l~D~~~~V 193 (228)
T PF12348_consen 116 NALDAIIESCS-YSPKILLEILSQGLKSKNPQVREECAEWLAIILEKWGSDSSVLQ-KSAFLKQLVKALVKLLSDADPEV 193 (228)
T ss_dssp HHHHHHHTTS--H--HHHHHHHHHHTT-S-HHHHHHHHHHHHHHHTT-----GGG---HHHHHHHHHHHHHHHTSS-HHH
T ss_pred HHHHHHHHHCC-cHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHccchHhhhc-ccchHHHHHHHHHHHCCCCCHHH
Confidence 34444444444 1234457888888899999999999998998888776 22221 12234455578899999999999
Q ss_pred HHHHHHHHHHhcc
Q 005358 367 REKANKVLSLLGE 379 (700)
Q Consensus 367 ReKA~KVL~lLg~ 379 (700)
|+.|++++..|--
T Consensus 194 R~~Ar~~~~~l~~ 206 (228)
T PF12348_consen 194 REAARECLWALYS 206 (228)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 9999999988843
No 35
>cd03562 CID CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1. Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.
Probab=89.14 E-value=3.2 Score=37.86 Aligned_cols=106 Identities=18% Similarity=0.275 Sum_probs=69.3
Q ss_pred HHHHHHHHhhcCCcccCCCHHHHHHHHHHHhhcCHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHHHHHH
Q 005358 269 EEKLLETIVTYGGVRLQPTRDAIQVFLVEAAKLDALAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSIILSYF 348 (700)
Q Consensus 269 E~~LVe~i~T~gGvr~~PSreeLq~Fl~~c~~Ld~e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~Yf 348 (700)
+..+++++.+.- -..|+-..|..++.+-.. .+..|++++.++|...+=..++-+|+++..+++...... ..+|
T Consensus 4 ~~~~l~~L~~~~--~S~~~I~~lt~~a~~~~~-~a~~iv~~i~~~i~~~~~~~KL~~LYL~dsIvkn~~~~~----~~~~ 76 (114)
T cd03562 4 YNALLEKLTFNK--NSQPSIQTLTKLAIENRK-HAKEIVEIIEKHIKKCPPEQKLPLLYLLDSIVKNVGRKY----KEFF 76 (114)
T ss_pred HHHHHHHHHcCc--ccHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHhCCcccchHHHHHHHHHHHHcccch----HHHH
Confidence 445566655431 122333334444444433 567899999999965444789999999999999865432 2344
Q ss_pred Hhh-hHHHhhhhcCCChhHHHHHHHHHHHhcccc
Q 005358 349 CEN-NDVVVKCSESPQSSLREKANKVLSLLGEEQ 381 (700)
Q Consensus 349 ~eN-~~~L~r~~~s~q~~LReKA~KVL~lLg~~~ 381 (700)
.+. .+.+..........+|+|..||+..+.-..
T Consensus 77 ~~~~~~~f~~~~~~~~~~~r~kl~rl~~iW~~~~ 110 (114)
T cd03562 77 SEFLVPLFLDAYEKVDEKTRKKLERLLNIWEERF 110 (114)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHHccCCC
Confidence 443 455555556778899999999999886543
No 36
>PF12755 Vac14_Fab1_bd: Vacuolar 14 Fab1-binding region
Probab=87.66 E-value=4.8 Score=36.69 Aligned_cols=73 Identities=25% Similarity=0.198 Sum_probs=57.4
Q ss_pred CHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHHHHHHHhhhHHHhhhhcCCChhHHHHHHHHHHHhc
Q 005358 302 DALAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSIILSYFCENNDVVVKCSESPQSSLREKANKVLSLLG 378 (700)
Q Consensus 302 d~e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~Yf~eN~~~L~r~~~s~q~~LReKA~KVL~lLg 378 (700)
-.+.|++.+...+.++.|+||+=|.=+|=-|.+... ..+..||.+-=+.|.++...+...||.-|.-+-++|.
T Consensus 24 ~l~~Il~pVL~~~~D~d~rVRy~AcEaL~ni~k~~~----~~~l~~f~~IF~~L~kl~~D~d~~Vr~~a~~Ld~llk 96 (97)
T PF12755_consen 24 YLDEILPPVLKCFDDQDSRVRYYACEALYNISKVAR----GEILPYFNEIFDALCKLSADPDENVRSAAELLDRLLK 96 (97)
T ss_pred HHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhc
Confidence 346788888899999999999876655444444332 3556788888899999999999999999988888875
No 37
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=87.64 E-value=1.9 Score=50.87 Aligned_cols=108 Identities=24% Similarity=0.313 Sum_probs=79.5
Q ss_pred HhhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHHHH--HH
Q 005358 14 SRMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREM--QR 91 (700)
Q Consensus 14 ~~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r~l--rr 91 (700)
.+++.+||+..---.--=.+-||..+++.--. -++.-|.-+-+|+++..|||+.=+|+++++||.++...|+.++ |.
T Consensus 10 ~~l~~~at~~~~~~~~~e~~~e~~d~ir~~~~-~~k~slr~~~~~i~h~np~~~~~~~~~~d~cvkn~G~gv~~ei~tre 88 (634)
T KOG1818|consen 10 KRLIEKATSETLGSGDWEAILEISDMIRSGGV-PPKPSLRGIKKRIDHENPNVQLFTLKLTDHCVKNCGHGVHCEIATRE 88 (634)
T ss_pred HhhhhhhhhhhhcCcchhhhhhHHHHHHhcCC-CCchhHHHHHHHHhccCCCcccchhhhHHHHHhcCCcchhHHHHHHH
Confidence 37889999887733333467789999987654 3678899999999999999999999999999998876666554 44
Q ss_pred hHHHHHHhhcccCCCCCCCCchhhHHHHHHHHHHHHHhhc
Q 005358 92 HSAVVRQLFHYKGQLDPLKGDALNKAVRDMAHEAISAIFS 131 (700)
Q Consensus 92 ns~~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll~aLf~ 131 (700)
....++.|..-.- .+.-||..-.+++..++.
T Consensus 89 ~m~~~~~~l~~~~---------~~e~v~~~~l~~~q~wa~ 119 (634)
T KOG1818|consen 89 FMDLLKSLLESQR---------IHEEVKNKILELIQNWAA 119 (634)
T ss_pred HHHHHHhhhcccc---------ccchHHHHHHHHHHHHHH
Confidence 4566777664442 334466666666666655
No 38
>cd03564 ANTH_AP180_CALM ANTH domain family; composed of adaptor protein 180 (AP180), clathrin assembly lymphoid myeloid leukemia protein (CALM) and similar proteins. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. AP180 and CALM play important roles in clathrin-mediated endocytosis. AP180 is a brain-specific clathrin-binding protein which stimulates clathrin assembly during the recycling of synaptic vesicles. The ANTH domain is structurally similar to the VHS domain and is composed of a superhelix of eight alpha helices. ANTH domains bind both inositol phospholipids and proteins, and contribute to the nucleation and formation of clathrin coats on membranes. ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that the ANTH domain is a universal component of the machine
Probab=86.89 E-value=4.6 Score=37.38 Aligned_cols=56 Identities=20% Similarity=0.376 Sum_probs=48.4
Q ss_pred ccCCCHHHHHHHHHHHhh--cCHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCc
Q 005358 283 RLQPTRDAIQVFLVEAAK--LDALAMSRALEAKLQSPLWQVRMKAICVLESILRKKDD 338 (700)
Q Consensus 283 r~~PSreeLq~Fl~~c~~--Ld~e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~ 338 (700)
-..|...-++.-+..+.. -++..+..+|.++|....|.+-+|+|.+|..||+.+..
T Consensus 13 ~~~pk~k~v~~ii~~t~~~~~~~~~~~~~l~~Rl~~~~w~v~~K~LillH~llr~G~~ 70 (117)
T cd03564 13 EAPPKDKHVRKIIAGTSSSPASIPSFASALSRRLLDRNWVVVLKALILLHRLLREGHP 70 (117)
T ss_pred CCCCChHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCcHHHHHHHHHHHHHHHhcCCH
Confidence 566777777777777766 78899999999999889999999999999999998864
No 39
>PF12348 CLASP_N: CLASP N terminal; InterPro: IPR024395 This domain is found in the N-terminal region of CLIP-associated proteins (CLASPs), which are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules [, ]. The domain is also found in other proteins involved in microtubule binding, including STU1, MOR1 and spindle pole body component Alp14.; PDB: 2QK2_A.
Probab=86.21 E-value=3.7 Score=41.06 Aligned_cols=69 Identities=19% Similarity=0.378 Sum_probs=38.0
Q ss_pred HHHHHHhhccCCCchHHHHHHHHHHHHhcCC---hhhHHH--HHHhHHHHHHhhcccCCCCCCCCchhhHHHHHHHHHHH
Q 005358 52 SDFILKRLEHKSPVVKQKALRLIKYSVGKSG---TDFRRE--MQRHSAVVRQLFHYKGQLDPLKGDALNKAVRDMAHEAI 126 (700)
Q Consensus 52 ~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs---~~F~r~--lrrns~~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll 126 (700)
..+|..-+++|+|.|+.-|+.+|..++..-. ..+... +..-...|..+. . +....||+.|++++
T Consensus 133 ~~~l~~~~~~Kn~~vR~~~~~~l~~~l~~~~~~~~~l~~~~~~~~l~~~l~~~l---~--------D~~~~VR~~Ar~~~ 201 (228)
T PF12348_consen 133 LEILSQGLKSKNPQVREECAEWLAIILEKWGSDSSVLQKSAFLKQLVKALVKLL---S--------DADPEVREAARECL 201 (228)
T ss_dssp HHHHHHHTT-S-HHHHHHHHHHHHHHHTT-----GGG--HHHHHHHHHHHHHHH---T--------SS-HHHHHHHHHHH
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHHHHccchHhhhcccchHHHHHHHHHHHC---C--------CCCHHHHHHHHHHH
Confidence 5666666666666676667766666665444 333221 222223333333 1 23456999999999
Q ss_pred HHhhc
Q 005358 127 SAIFS 131 (700)
Q Consensus 127 ~aLf~ 131 (700)
..++.
T Consensus 202 ~~l~~ 206 (228)
T PF12348_consen 202 WALYS 206 (228)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 99987
No 40
>KOG1087 consensus Cytosolic sorting protein GGA2/TOM1 [Intracellular trafficking, secretion, and vesicular transport]
Probab=84.08 E-value=6 Score=45.57 Aligned_cols=107 Identities=19% Similarity=0.212 Sum_probs=72.8
Q ss_pred HHHHHHHhhcCCcccCCCHHHHHHHHHHHhhcCH-----HHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHH
Q 005358 270 EKLLETIVTYGGVRLQPTRDAIQVFLVEAAKLDA-----LAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSII 344 (700)
Q Consensus 270 ~~LVe~i~T~gGvr~~PSreeLq~Fl~~c~~Ld~-----e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v 344 (700)
.++|+. .|. . ....+.+.-+++=|-.+|. ..++.+|.+||++..=.+++.||.+||.+++..+.-++..|
T Consensus 3 ~~~Idk-AT~-~---~l~~pDWa~NleIcD~IN~~~~~~~eAvralkKRi~~k~s~vq~lALtlLE~cvkNCG~~fh~~V 77 (470)
T KOG1087|consen 3 GKLIDK-ATS-E---SLAEPDWALNLEICDLINSTEGGPKEAVRALKKRLNSKNSKVQLLALTLLETCVKNCGYSFHLQV 77 (470)
T ss_pred HHHHHH-hhc-c---cccCccHHHHHHHHHHHhcCccCcHHHHHHHHHHhccCCcHHHHHHHHHHHHHHHhhhHHHHHHH
Confidence 356666 333 1 2234456666777766654 57888999999755557999999999999998775544233
Q ss_pred H-HHHHhhhHHHhhhhcC-CChhHHHHHHHHHHHhcccccC
Q 005358 345 L-SYFCENNDVVVKCSES-PQSSLREKANKVLSLLGEEQAG 383 (700)
Q Consensus 345 ~-~Yf~eN~~~L~r~~~s-~q~~LReKA~KVL~lLg~~~~~ 383 (700)
+ .=|. .+-|++-... +...||+|+--+|..|+-...+
T Consensus 78 a~k~fL--~emVk~~k~~~~~~~Vr~kiL~LI~~W~~af~~ 116 (470)
T KOG1087|consen 78 ASKEFL--NEMVKRPKNKPRDLKVREKILELIDTWQQAFCG 116 (470)
T ss_pred HHHHHH--HHHHhccccCCcchhHHHHHHHHHHHHHHHccC
Confidence 3 2232 1245555555 6678999999999988887777
No 41
>cd06224 REM Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately N-terminal to the RasGef (Cdc25-like) domain. REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins with the REM domain include Sos1 and Sos2, which relay signals from tyrosine-kinase mediated signalling to Ras, RasGRP1-4, RasGRF1,2, CNrasGEF, and RAP-specific nucleotide exchange factors, to name a few.
Probab=80.08 E-value=3.9 Score=36.97 Aligned_cols=69 Identities=20% Similarity=0.214 Sum_probs=53.4
Q ss_pred hhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccCC--------------CchHHHHHHHHHHHHhc
Q 005358 15 RMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKS--------------PVVKQKALRLIKYSVGK 80 (700)
Q Consensus 15 ~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks--------------~hVKlKaLKILkyLc~~ 80 (700)
.||...|+.+. .+..-|.++-=+||.+-.+. .++++.|..|.+... ..|+.+++++|++-+.+
T Consensus 4 ~Li~~L~~~~~--~~d~~f~~~FllTyrsF~s~-~~ll~~L~~rf~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~Wv~~ 80 (122)
T cd06224 4 ALIEHLTSTFD--MPDPSFVSTFLLTYRSFTTP-TELLEKLIERYEIAPPENLEYNDWDKKKSKPIRLRVLNVLRTWVEN 80 (122)
T ss_pred HHHHHHcCCCc--cccHHHHHHHHHHhhhhCCH-HHHHHHHHHHhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 57888888776 44555666666777775543 699999999999553 23788999999999999
Q ss_pred CChhhH
Q 005358 81 SGTDFR 86 (700)
Q Consensus 81 Gs~~F~ 86 (700)
-..+|.
T Consensus 81 ~~~df~ 86 (122)
T cd06224 81 YPYDFF 86 (122)
T ss_pred CCCccc
Confidence 999985
No 42
>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=79.48 E-value=3.7 Score=29.49 Aligned_cols=29 Identities=28% Similarity=0.210 Sum_probs=23.9
Q ss_pred HHHHHHHHhCCchHHHHHHHHHHHHHHHh
Q 005358 306 MSRALEAKLQSPLWQVRMKAICVLESILR 334 (700)
Q Consensus 306 V~elL~~kL~~~~WQvrlRALcvIEaLl~ 334 (700)
|+..|.+-|+++.|.||.-|+.+|..|.+
T Consensus 1 llp~l~~~l~D~~~~VR~~a~~~l~~i~~ 29 (31)
T PF02985_consen 1 LLPILLQLLNDPSPEVRQAAAECLGAIAE 29 (31)
T ss_dssp HHHHHHHHHT-SSHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Confidence 45677788899999999999999988875
No 43
>KOG2374 consensus Uncharacterized conserved protein [Function unknown]
Probab=79.46 E-value=20 Score=41.78 Aligned_cols=111 Identities=17% Similarity=0.139 Sum_probs=87.7
Q ss_pred hhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHHHHHHhHH
Q 005358 15 RMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREMQRHSA 94 (700)
Q Consensus 15 ~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrrns~ 94 (700)
.+|+++|-+..--.---+|.+|-++++.|.+ .|.-....|+.-+.+.++-|.+=+|.|+.-|.- .++-|+..+..|..
T Consensus 10 ~lIeelT~sg~~~~~p~~~k~lkkiv~~sde-e~~~~~~~L~~~~~~~h~~vR~l~lqii~elF~-rs~~FR~lii~n~~ 87 (661)
T KOG2374|consen 10 GLIEELTKSGAQEVDPRLLKALKKIVRYSDE-EVRLSSQTLMELMRHNHSQVRYLTLQIIDELFM-RSKLFRTLIIENLD 87 (661)
T ss_pred HHHHHHhhcCCcccChHHHHHHHHHHhccHH-HHHHHHHHHHHHHhhcCchHHHHHHHHHHHHHH-hhHHHHHHHHhCHH
Confidence 6788888877766667799999999999875 488889999999999999999999999999876 57899999999988
Q ss_pred HHHHhhcccCCCCCCCCc-hhhHHHHHHHHHHHH
Q 005358 95 VVRQLFHYKGQLDPLKGD-ALNKAVRDMAHEAIS 127 (700)
Q Consensus 95 ~IK~l~~F~GppDpl~Gd-~l~q~VR~~AkEll~ 127 (700)
..-+|.-=.-|--||-+- ...+..|.+|-++++
T Consensus 88 efLeL~~gt~p~~PLP~p~~~a~~Lr~~ai~~~e 121 (661)
T KOG2374|consen 88 EFLELSIGTRPNLPLPAPPAVATTLRSKAIEFLE 121 (661)
T ss_pred HHHHHhhcCCCCCCCCCChHHHHHHHHHHHHHHH
Confidence 777765433343455442 345568888877765
No 44
>KOG2374 consensus Uncharacterized conserved protein [Function unknown]
Probab=79.06 E-value=17 Score=42.30 Aligned_cols=105 Identities=19% Similarity=0.251 Sum_probs=78.2
Q ss_pred hHHHHHHHHhhcCCcccCCCHHHHHHHHHHHhhcC--HHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHHH
Q 005358 268 REEKLLETIVTYGGVRLQPTRDAIQVFLVEAAKLD--ALAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSIIL 345 (700)
Q Consensus 268 ~E~~LVe~i~T~gGvr~~PSreeLq~Fl~~c~~Ld--~e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~ 345 (700)
.-.+||++++++|-.++-| ..++..-+.|..-| |+.+.+.|...|....-|+|+-+|-.|+.|+-+. .+..
T Consensus 7 kl~~lIeelT~sg~~~~~p--~~~k~lkkiv~~sdee~~~~~~~L~~~~~~~h~~vR~l~lqii~elF~rs-----~~FR 79 (661)
T KOG2374|consen 7 KLIGLIEELTKSGAQEVDP--RLLKALKKIVRYSDEEVRLSSQTLMELMRHNHSQVRYLTLQIIDELFMRS-----KLFR 79 (661)
T ss_pred HHHHHHHHHhhcCCcccCh--HHHHHHHHHHhccHHHHHHHHHHHHHHHhhcCchHHHHHHHHHHHHHHhh-----HHHH
Confidence 4578999999998888876 45566666665544 5778889999998888899999999999988653 2335
Q ss_pred HHHHhhhHHHhhhhcCCC------------hhHHHHHHHHHHHhcc
Q 005358 346 SYFCENNDVVVKCSESPQ------------SSLREKANKVLSLLGE 379 (700)
Q Consensus 346 ~Yf~eN~~~L~r~~~s~q------------~~LReKA~KVL~lLg~ 379 (700)
....+|-+.+..|+-.-. ..||.+|.++|.-|+.
T Consensus 80 ~lii~n~~efLeL~~gt~p~~PLP~p~~~a~~Lr~~ai~~~e~Wne 125 (661)
T KOG2374|consen 80 TLIIENLDEFLELSIGTRPNLPLPAPPAVATTLRSKAIEFLEKWNE 125 (661)
T ss_pred HHHHhCHHHHHHHhhcCCCCCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 556777777777664322 3589999999887653
No 45
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=78.46 E-value=15 Score=30.89 Aligned_cols=73 Identities=19% Similarity=0.079 Sum_probs=49.2
Q ss_pred HHHHHHHHHHHhhcCHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHHHHHHHhhhHHHhh-hhcCCChhH
Q 005358 288 RDAIQVFLVEAAKLDALAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSIILSYFCENNDVVVK-CSESPQSSL 366 (700)
Q Consensus 288 reeLq~Fl~~c~~Ld~e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~Yf~eN~~~L~r-~~~s~q~~L 366 (700)
...-..-++....+..+.+.+.|..-|+++.|.||..|+-+|..+-... . .+.|.+ +.++....+
T Consensus 14 ~~vr~~a~~~L~~~~~~~~~~~L~~~l~d~~~~vr~~a~~aL~~i~~~~---~-----------~~~L~~~l~~~~~~~v 79 (88)
T PF13646_consen 14 PQVRAEAARALGELGDPEAIPALIELLKDEDPMVRRAAARALGRIGDPE---A-----------IPALIKLLQDDDDEVV 79 (88)
T ss_dssp HHHHHHHHHHHHCCTHHHHHHHHHHHHTSSSHHHHHHHHHHHHCCHHHH---T-----------HHHHHHHHTC-SSHHH
T ss_pred HHHHHHHHHHHHHcCCHhHHHHHHHHHcCCCHHHHHHHHHHHHHhCCHH---H-----------HHHHHHHHcCCCcHHH
Confidence 3333445555567788889999999999999999999998888764211 1 133444 444455667
Q ss_pred HHHHHHHH
Q 005358 367 REKANKVL 374 (700)
Q Consensus 367 ReKA~KVL 374 (700)
|..|.+.|
T Consensus 80 r~~a~~aL 87 (88)
T PF13646_consen 80 REAAAEAL 87 (88)
T ss_dssp HHHHHHHH
T ss_pred HHHHHhhc
Confidence 88887765
No 46
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=76.50 E-value=7.5 Score=32.68 Aligned_cols=60 Identities=23% Similarity=0.221 Sum_probs=43.3
Q ss_pred HHHHHHHh-CCchHHHHHHHHHHHHHHHhccCchhHHHHHHHHHhhhHHHhhhhcCCChhHHHHHHHHHHHhccc
Q 005358 307 SRALEAKL-QSPLWQVRMKAICVLESILRKKDDEKFSIILSYFCENNDVVVKCSESPQSSLREKANKVLSLLGEE 380 (700)
Q Consensus 307 ~elL~~kL-~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~Yf~eN~~~L~r~~~s~q~~LReKA~KVL~lLg~~ 380 (700)
++.|.+.| .++.|.+|..|+-+|. +.+.. .+ .+.|..+..++...||..|-..|..+|.+
T Consensus 1 i~~L~~~l~~~~~~~vr~~a~~~L~---~~~~~----~~-------~~~L~~~l~d~~~~vr~~a~~aL~~i~~~ 61 (88)
T PF13646_consen 1 IPALLQLLQNDPDPQVRAEAARALG---ELGDP----EA-------IPALIELLKDEDPMVRRAAARALGRIGDP 61 (88)
T ss_dssp HHHHHHHHHTSSSHHHHHHHHHHHH---CCTHH----HH-------HHHHHHHHTSSSHHHHHHHHHHHHCCHHH
T ss_pred CHHHHHHHhcCCCHHHHHHHHHHHH---HcCCH----hH-------HHHHHHHHcCCCHHHHHHHHHHHHHhCCH
Confidence 35677777 8999999998877776 22211 11 24455666788899999999999998743
No 47
>PF12830 Nipped-B_C: Sister chromatid cohesion C-terminus
Probab=74.42 E-value=14 Score=37.00 Aligned_cols=60 Identities=30% Similarity=0.300 Sum_probs=49.6
Q ss_pred CCchHHHHHHHHHHHHHHHhccCchhHHHHHHHHHhhhHHHhhhhcCCChhHHHHHHHHHHHhccccc
Q 005358 315 QSPLWQVRMKAICVLESILRKKDDEKFSIILSYFCENNDVVVKCSESPQSSLREKANKVLSLLGEEQA 382 (700)
Q Consensus 315 ~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~Yf~eN~~~L~r~~~s~q~~LReKA~KVL~lLg~~~~ 382 (700)
-++.-++|+.|+.+|+.+++.+-.-+.+ .-+.|+.|..++...+|++|.++|+.|..--+
T Consensus 18 ~~~~~~vr~~Al~~l~~il~qGLvnP~~--------cvp~lIAL~ts~~~~ir~~A~~~l~~l~eK~~ 77 (187)
T PF12830_consen 18 LSSDDSVRLAALQVLELILRQGLVNPKQ--------CVPTLIALETSPNPSIRSRAYQLLKELHEKHE 77 (187)
T ss_pred hCCCHHHHHHHHHHHHHHHhcCCCChHH--------HHhHhhhhhCCCChHHHHHHHHHHHHHHHHhH
Confidence 3667789999999999999998655533 34778899999999999999999999865443
No 48
>smart00582 RPR domain present in proteins, which are involved in regulation of nuclear pre-mRNA.
Probab=73.45 E-value=18 Score=33.12 Aligned_cols=94 Identities=14% Similarity=0.118 Sum_probs=57.6
Q ss_pred CCHHHHHHHHHHHhh--cCHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHH-HHHHHhhhHHHhhhhcCC
Q 005358 286 PTRDAIQVFLVEAAK--LDALAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSII-LSYFCENNDVVVKCSESP 362 (700)
Q Consensus 286 PSreeLq~Fl~~c~~--Ld~e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v-~~Yf~eN~~~L~r~~~s~ 362 (700)
++++.|+.-..-|-. -....|++++.+++...+=..|+-.|+++..+++.......... ..|...=.+.+.......
T Consensus 11 ~s~~~I~~lt~~~~~~~~~a~~Iv~~i~~~~~~~~~~~kL~~LYlindIl~n~~~~~~~~f~~~~~~~~~~~~~~~~~~~ 90 (121)
T smart00582 11 NSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPPPRKLPLLYLLDSIVQNSKRKYGSEFGDELGPVFQDALRDVLGAA 90 (121)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccceehhHHhHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHhC
Confidence 566666655544443 14467999999999433335888899999999997643211111 111111113333444444
Q ss_pred ChhHHHHHHHHHHHhcc
Q 005358 363 QSSLREKANKVLSLLGE 379 (700)
Q Consensus 363 q~~LReKA~KVL~lLg~ 379 (700)
+...|.|..|||+.+.-
T Consensus 91 ~~~~~~ki~kll~iW~~ 107 (121)
T smart00582 91 NDETKKKIRRLLNIWEE 107 (121)
T ss_pred CHHHHHHHHHHHHHHhc
Confidence 46799999999999875
No 49
>cd03562 CID CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1. Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.
Probab=73.19 E-value=25 Score=31.99 Aligned_cols=98 Identities=13% Similarity=0.238 Sum_probs=64.5
Q ss_pred hhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHHHHHHh-HH
Q 005358 16 MIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREMQRH-SA 94 (700)
Q Consensus 16 lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrrn-s~ 94 (700)
.+++-|... ...=...++..++.+.. ....+|++.+.+++++..|.-|+=+|=|++-+|++............ ..
T Consensus 7 ~l~~L~~~~---~S~~~I~~lt~~a~~~~-~~a~~iv~~i~~~i~~~~~~~KL~~LYL~dsIvkn~~~~~~~~~~~~~~~ 82 (114)
T cd03562 7 LLEKLTFNK---NSQPSIQTLTKLAIENR-KHAKEIVEIIEKHIKKCPPEQKLPLLYLLDSIVKNVGRKYKEFFSEFLVP 82 (114)
T ss_pred HHHHHHcCc---ccHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHhCCcccchHHHHHHHHHHHHcccchHHHHHHHHHH
Confidence 344444444 44556677777776654 45689999999999999999999999999999987655555544444 33
Q ss_pred HHHHhhcccCCCCCCCCchhhHHHHHHHHHHHHH
Q 005358 95 VVRQLFHYKGQLDPLKGDALNKAVRDMAHEAISA 128 (700)
Q Consensus 95 ~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll~a 128 (700)
++..+. +.. ...+|.+-+.|++.
T Consensus 83 ~f~~~~--~~~---------~~~~r~kl~rl~~i 105 (114)
T cd03562 83 LFLDAY--EKV---------DEKTRKKLERLLNI 105 (114)
T ss_pred HHHHHH--HhC---------CHHHHHHHHHHHHH
Confidence 333222 222 23367766666654
No 50
>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=73.18 E-value=8.9 Score=30.24 Aligned_cols=55 Identities=20% Similarity=0.171 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHHHHHhccCchhHHHHHHHHHhhhHHHhhhhcCCChhHHHHHHHHHHHh
Q 005358 319 WQVRMKAICVLESILRKKDDEKFSIILSYFCENNDVVVKCSESPQSSLREKANKVLSLL 377 (700)
Q Consensus 319 WQvrlRALcvIEaLl~s~~~d~~~~v~~Yf~eN~~~L~r~~~s~q~~LReKA~KVL~lL 377 (700)
|.||..|+.+|-.|.+... ..+..|..+--+.|..+-..+...||..|-.-|..|
T Consensus 1 p~vR~~A~~aLg~l~~~~~----~~~~~~~~~~~~~L~~~L~d~~~~VR~~A~~aLg~l 55 (55)
T PF13513_consen 1 PRVRRAAAWALGRLAEGCP----ELLQPYLPELLPALIPLLQDDDDSVRAAAAWALGNL 55 (55)
T ss_dssp HHHHHHHHHHHHCTTTTTH----HHHHHHHHHHHHHHHHHTTSSSHHHHHHHHHHHHCH
T ss_pred CHHHHHHHHHHhhHhcccH----HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhcC
Confidence 8999999998866554332 244566777778888888888889999998777543
No 51
>PF00618 RasGEF_N: RasGEF N-terminal motif; InterPro: IPR000651 The crystal structure of the guanine nucleotide exchange factor (GEF) region of human Sos1 complexes with Ras has been solved []. The structure consists of two distinct alpha helical structural domains: the N-terminal domain which seems to have a purely structural role and the C-terminal domain which is sufficient for catalytic activity and contains all residues that interact with Ras. A main feature of the catalytic domain is the protrusion of a helical hairpin important for the nucleotide-exchange mechanism. The N-terminal domain is likely to be important for the stability and correct placement of the hairpin structure. This entry represents a domain found in several GEF for Ras-like small GTPases which lies N-terminal to the RasGef (Cdc25-like) domain. ; GO: 0005085 guanyl-nucleotide exchange factor activity, 0051056 regulation of small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3CF6_E 2BYV_E 1NVW_S 1BKD_S 1XDV_A 2II0_A 1NVU_S 1NVX_S 1NVV_S 1XD4_B ....
Probab=73.00 E-value=10 Score=33.78 Aligned_cols=73 Identities=21% Similarity=0.325 Sum_probs=50.0
Q ss_pred hhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccCCC---------------chHHHHHHHHHHHHh
Q 005358 15 RMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKSP---------------VVKQKALRLIKYSVG 79 (700)
Q Consensus 15 ~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks~---------------hVKlKaLKILkyLc~ 79 (700)
.||.+.|+..... -..|-+.-=+||.+-.+ -.++++.|..|.+...+ .|+.|++++|++.+.
T Consensus 9 ~Li~~L~~~~~~~--d~~f~~~FllTyr~F~t-p~~Ll~~L~~ry~~~~~~~~~~~~~~~~~~~~~i~~rv~~~l~~Wi~ 85 (104)
T PF00618_consen 9 KLIERLTSSFNSD--DEEFVDTFLLTYRSFTT-PEELLDKLIQRYNIPPPNGLSQDESWDQDSQEPIRLRVLNVLKYWIE 85 (104)
T ss_dssp HHHHHHCHC-SS---HHHHHHHHHHHHHHCS--HHHHHHHHHHHHT---SSS-HHHHT-HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhcccccC--CHHHHHHHHHHhHhhCC-HHHHHHHHHHHhcccCCccccccchhhhhhhHHHHHHHHHHHHHHHH
Confidence 6788888774444 23566666677776543 36999999999953222 278899999999998
Q ss_pred cCChhhHHHHH
Q 005358 80 KSGTDFRREMQ 90 (700)
Q Consensus 80 ~Gs~~F~r~lr 90 (700)
+-..+|.....
T Consensus 86 ~~~~df~~~~~ 96 (104)
T PF00618_consen 86 NYPDDFRDDPE 96 (104)
T ss_dssp HHCCCCHH-HH
T ss_pred HChHhhCCCHH
Confidence 88778887754
No 52
>PF11467 LEDGF: Lens epithelium-derived growth factor (LEDGF) ; InterPro: IPR021567 LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis. It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alpha-helices. The residues essential for the interaction with the integrase are present in the inter-helical loop regions of the bundle structure. ; PDB: 3F9K_K 3HPG_G 3U88_C 3HPH_H 2B4J_D 1Z9E_A.
Probab=70.36 E-value=12 Score=35.10 Aligned_cols=69 Identities=23% Similarity=0.339 Sum_probs=45.3
Q ss_pred HHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHHHHHHhHH---HHHHhhcccCCCCCCCCchhhHHHHHHHHHHH
Q 005358 50 EVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREMQRHSA---VVRQLFHYKGQLDPLKGDALNKAVRDMAHEAI 126 (700)
Q Consensus 50 eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrrns~---~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll 126 (700)
+|---|-.-|.-..|.| -|||.+|+-|-.= +-=..-|+||.. .||.|+.|.|. +.||+.|.++-
T Consensus 6 ~l~~~Ik~~L~~~~~Dv-~kcL~~LdeL~~l--~vT~~mL~kn~e~V~TlkklRrY~gn----------~~Ir~KA~~lY 72 (106)
T PF11467_consen 6 ELHSEIKSSLKVDNPDV-KKCLKALDELKSL--QVTSLMLQKNPECVETLKKLRRYKGN----------QQIRKKATELY 72 (106)
T ss_dssp HHHHHHHHTCETTEE-H-HHHHHHHHHHHTS-----HHHHTTTHHHHHHHHHHTT-TT-----------HHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCCCH-HHHHHHHHHHhcc--CCCHHHHHhCHHHHHHHHHHHHhhcc----------HHHHHHHHHHH
Confidence 44444555666667888 8999999988643 111345677775 46667888885 78999999995
Q ss_pred H---Hhhc
Q 005358 127 S---AIFS 131 (700)
Q Consensus 127 ~---aLf~ 131 (700)
+ .+|-
T Consensus 73 nkfK~~f~ 80 (106)
T PF11467_consen 73 NKFKSLFL 80 (106)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHhC
Confidence 4 5663
No 53
>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=69.20 E-value=21 Score=32.82 Aligned_cols=82 Identities=21% Similarity=0.249 Sum_probs=57.9
Q ss_pred hhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccCCCc-----------hHHHHHHHHHHHHhcCCh
Q 005358 15 RMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKSPV-----------VKQKALRLIKYSVGKSGT 83 (700)
Q Consensus 15 ~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks~h-----------VKlKaLKILkyLc~~Gs~ 83 (700)
.||...|..+..+ -.-|-++==+||.+-.+ ..++++.|..|.....+. +|.+++++|++.+.+-..
T Consensus 12 ~Li~~L~~~~~~~--d~~f~~~Flltyr~F~t-p~~ll~~L~~rf~~~~~~~~~~~~~~~~~~~~rv~~~l~~Wv~~~~~ 88 (127)
T smart00229 12 KLIEHLTEAFDKA--DPFFVETFLLTYRSFIT-TQELLQLLLYRYNAIPPESWVERKVNPLRVKNRVLNILRHWVENYWQ 88 (127)
T ss_pred HHHHHHcCCCcCC--CHHHHHHHHHHhhhhCC-HHHHHHHHHHHhCCCCcHHHHHHHhhHHHHHHHHHHHHHHHHHHCCc
Confidence 5677777766543 34455555567766543 469999999999966543 788999999999998888
Q ss_pred hhHHH--HHHhHH-HHHHh
Q 005358 84 DFRRE--MQRHSA-VVRQL 99 (700)
Q Consensus 84 ~F~r~--lrrns~-~IK~l 99 (700)
+|... +.+... ++...
T Consensus 89 dF~~~~~l~~~l~~f~~~~ 107 (127)
T smart00229 89 DFEDDPKLILRLLEFLDLV 107 (127)
T ss_pred ccccCHHHHHHHHHHHHHH
Confidence 89877 455543 44443
No 54
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=68.57 E-value=22 Score=35.03 Aligned_cols=71 Identities=18% Similarity=0.112 Sum_probs=54.3
Q ss_pred HHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHHHHHHHhhhHHHhhhhcCCChhHHHHHHHHHHHhcccc
Q 005358 304 LAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSIILSYFCENNDVVVKCSESPQSSLREKANKVLSLLGEEQ 381 (700)
Q Consensus 304 e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~Yf~eN~~~L~r~~~s~q~~LReKA~KVL~lLg~~~ 381 (700)
+.....|..+|+++.+.||..||.+|-.|+..+-...-..+ | ..+..|...+...||+-|...+..+....
T Consensus 24 e~~~~~l~~~L~D~~~~VR~~al~~Ls~Li~~d~ik~k~~l---~----~~~l~~l~D~~~~Ir~~A~~~~~e~~~~~ 94 (178)
T PF12717_consen 24 EPYLPNLYKCLRDEDPLVRKTALLVLSHLILEDMIKVKGQL---F----SRILKLLVDENPEIRSLARSFFSELLKKR 94 (178)
T ss_pred HhHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCceeehhhh---h----HHHHHHHcCCCHHHHHHHHHHHHHHHHhc
Confidence 56677888999999999999999999999987632211111 0 23556778888999999999999988763
No 55
>PF14500 MMS19_N: Dos2-interacting transcription regulator of RNA-Pol-II
Probab=67.54 E-value=26 Score=37.30 Aligned_cols=67 Identities=16% Similarity=0.164 Sum_probs=45.0
Q ss_pred CCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhc-CChhhHHHH
Q 005358 23 DEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGK-SGTDFRREM 89 (700)
Q Consensus 23 ddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~-Gs~~F~r~l 89 (700)
+|+.+-.--.+.+--+.+..+...+....+.+|+.||...++.||.=+|+.|..||.. |...+...+
T Consensus 181 ~dp~~IT~edLk~~L~~cl~s~~~fa~~~~p~LleKL~s~~~~~K~D~L~tL~~c~~~y~~~~~~~~~ 248 (262)
T PF14500_consen 181 NDPYGITREDLKRALRNCLSSTPLFAPFAFPLLLEKLDSTSPSVKLDSLQTLKACIENYGADSLSPHW 248 (262)
T ss_pred CCCCCCCHHHHHHHHHHHhcCcHhhHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHHHCCHHHHHHHH
Confidence 4443333333333334444443467789999999999999999999999999999864 433343333
No 56
>KOG0251 consensus Clathrin assembly protein AP180 and related proteins, contain ENTH domain [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=65.14 E-value=16 Score=42.50 Aligned_cols=68 Identities=21% Similarity=0.343 Sum_probs=50.7
Q ss_pred hHHHHHHHHhhcCCcccCCCHHHHHHHHHHHhh---cCHHHHHHHHHHHhCCc-hHHHHHHHHHHHHHHHhccCch
Q 005358 268 REEKLLETIVTYGGVRLQPTRDAIQVFLVEAAK---LDALAMSRALEAKLQSP-LWQVRMKAICVLESILRKKDDE 339 (700)
Q Consensus 268 ~E~~LVe~i~T~gGvr~~PSreeLq~Fl~~c~~---Ld~e~V~elL~~kL~~~-~WQvrlRALcvIEaLl~s~~~d 339 (700)
.|..+|+. | --...|+.+.--+++=.|.. -+...++++|.+||+.. .|.|-+|+|-+|=.||+.++..
T Consensus 24 l~~AV~KA--T--sh~~~ppk~k~l~~Il~~ts~~~~~i~~~v~aLs~Rl~~TrnW~VAlKsLIliH~ll~~G~~~ 95 (491)
T KOG0251|consen 24 LEKAVVKA--T--SHDDMPPKDKYLDEILSATSSSPASIPSCVHALSERLNKTRNWTVALKALILIHRLLKEGDPS 95 (491)
T ss_pred HHHHHHhh--c--cCCCCCccHHHHHHHHHHhcCCcccHHHHHHHHHHHhCCCcceeehHHHHHHHHHHHhcCcHH
Confidence 55555653 2 23466666666666655555 36799999999999877 9999999999999999877543
No 57
>PF08167 RIX1: rRNA processing/ribosome biogenesis
Probab=64.89 E-value=64 Score=31.74 Aligned_cols=93 Identities=22% Similarity=0.233 Sum_probs=63.4
Q ss_pred HHHHHhhcCCcccCCCHHHHHHHHHHHhhcCHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhH-HHHHHHHHh
Q 005358 272 LLETIVTYGGVRLQPTRDAIQVFLVEAAKLDALAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKF-SIILSYFCE 350 (700)
Q Consensus 272 LVe~i~T~gGvr~~PSreeLq~Fl~~c~~Ld~e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~-~~v~~Yf~e 350 (700)
+++.+...+-+...|+..++++++.+ +..-|+++.+..|..++|.+-.+++...-+.+ +.+..|++.
T Consensus 4 ll~~l~~~~~~~~~~~~~~l~~l~~r------------i~~LL~s~~~~~rw~G~~Ll~~~~~~~~~e~l~~~~~~W~~~ 71 (165)
T PF08167_consen 4 LLSTLRSCGLLLSAPSKSALHKLVTR------------INSLLQSKSAYSRWAGLCLLKVTVEQCSWEILLSHGSQWLRA 71 (165)
T ss_pred HHHHHHccchhhcccCHHHHHHHHHH------------HHHHhCCCChhhHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence 45555555555666767777777665 34445788888999999999999998755555 566667765
Q ss_pred hhHHHhhhhcCCChhHHHHHHHHHHHhcc
Q 005358 351 NNDVVVKCSESPQSSLREKANKVLSLLGE 379 (700)
Q Consensus 351 N~~~L~r~~~s~q~~LReKA~KVL~lLg~ 379 (700)
--..|++ .....+++-|-..|..|=.
T Consensus 72 Ll~~L~~---~~~~~~~~~ai~~L~~l~~ 97 (165)
T PF08167_consen 72 LLSILEK---PDPPSVLEAAIITLTRLFD 97 (165)
T ss_pred HHHHHcC---CCCHHHHHHHHHHHHHHHH
Confidence 5555554 4456677777777766643
No 58
>COG5098 Chromosome condensation complex Condensin, subunit D2 [Chromatin structure and dynamics / Cell division and chromosome partitioning]
Probab=63.06 E-value=25 Score=42.63 Aligned_cols=37 Identities=16% Similarity=0.317 Sum_probs=32.7
Q ss_pred hhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCC
Q 005358 46 SIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSG 82 (700)
Q Consensus 46 s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs 82 (700)
+.++.+|+.|-.||.+..|+++.|||.++.-+|...+
T Consensus 342 ~~~~~Lv~ll~ERl~D~~py~RtKalqv~~kifdl~s 378 (1128)
T COG5098 342 QKLNDLVGLLVERLSDTYPYTRTKALQVLEKIFDLNS 378 (1128)
T ss_pred HHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHhCcc
Confidence 3567899999999999999999999999999997443
No 59
>KOG1086 consensus Cytosolic sorting protein/ADP-ribosylation factor effector GGA [Intracellular trafficking, secretion, and vesicular transport]
Probab=62.50 E-value=38 Score=39.09 Aligned_cols=106 Identities=14% Similarity=0.279 Sum_probs=64.5
Q ss_pred hhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHHHHHHhHH--
Q 005358 17 IDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREMQRHSA-- 94 (700)
Q Consensus 17 V~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrrns~-- 94 (700)
|.+||.-...------+.-+|+-.++.++. -.-..+.|..+++...----+-||++|+||+.++.+.|..++-|.-.
T Consensus 13 lnrATdp~~~eedw~ai~~fceqinkdp~g-p~lAv~LlaHKiqSPqe~EAl~altvLe~cmkncGekfH~evgkfrFLN 91 (594)
T KOG1086|consen 13 LNRATDPSNDEEDWKAIDGFCEQINKDPEG-PLLAVRLLAHKIQSPQEWEALQALTVLEYCMKNCGEKFHEEVGKFRFLN 91 (594)
T ss_pred HHhccCccchHHHHHHHHHHHHHHhcCCCC-chhHHHHHHhhcCChhHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence 778886443222222233344444444432 12345566667776554445789999999999999999999877652
Q ss_pred -HHHHhhcccCCCCCCCCchhhHHHHHHHHHHHHHhhcC
Q 005358 95 -VVRQLFHYKGQLDPLKGDALNKAVRDMAHEAISAIFSE 132 (700)
Q Consensus 95 -~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll~aLf~d 132 (700)
.||-.. | .+-|+--..+|. .++|++||+=
T Consensus 92 ELIkvvs----P--KYlG~~tSekvK---tkiIelLfsW 121 (594)
T KOG1086|consen 92 ELIKVVS----P--KYLGSRTSEKVK---TKIIELLFSW 121 (594)
T ss_pred HHHHHhC----c--hhcchhhhHHHH---HHHHHHHhhh
Confidence 455433 1 234444444444 3689999993
No 60
>PF12755 Vac14_Fab1_bd: Vacuolar 14 Fab1-binding region
Probab=61.17 E-value=52 Score=30.02 Aligned_cols=73 Identities=14% Similarity=0.064 Sum_probs=50.3
Q ss_pred hhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHHHHHHhHHHHHHhhcccCCCCCCCCchhhHHHHHHHHHH
Q 005358 46 SIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREMQRHSAVVRQLFHYKGQLDPLKGDALNKAVRDMAHEA 125 (700)
Q Consensus 46 s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrrns~~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEl 125 (700)
...++|++-+++-+++....|++-|...|=.++.....++...+-.--. .+..-.. | +...||..|+-|
T Consensus 23 ~~l~~Il~pVL~~~~D~d~rVRy~AcEaL~ni~k~~~~~~l~~f~~IF~---~L~kl~~--D------~d~~Vr~~a~~L 91 (97)
T PF12755_consen 23 KYLDEILPPVLKCFDDQDSRVRYYACEALYNISKVARGEILPYFNEIFD---ALCKLSA--D------PDENVRSAAELL 91 (97)
T ss_pred HHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHc--C------CchhHHHHHHHH
Confidence 4567999999999999999999999999998887666666553333332 2222222 3 234599999655
Q ss_pred HHHh
Q 005358 126 ISAI 129 (700)
Q Consensus 126 l~aL 129 (700)
-.+|
T Consensus 92 d~ll 95 (97)
T PF12755_consen 92 DRLL 95 (97)
T ss_pred HHHh
Confidence 5544
No 61
>PRK09687 putative lyase; Provisional
Probab=61.02 E-value=29 Score=37.07 Aligned_cols=74 Identities=20% Similarity=0.218 Sum_probs=54.8
Q ss_pred HHHHHHHHHhhcCHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHHHHHHHhhhHHHhhhhcCCChhHHHH
Q 005358 290 AIQVFLVEAAKLDALAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSIILSYFCENNDVVVKCSESPQSSLREK 369 (700)
Q Consensus 290 eLq~Fl~~c~~Ld~e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~Yf~eN~~~L~r~~~s~q~~LReK 369 (700)
....|.+.|.+++.+.+.++|. ++...||..|+.+|..+- ..+-+ +.+.++..+....+|.-
T Consensus 12 ~~~~~~~~~~~~~~~~L~~~L~----d~d~~vR~~A~~aL~~~~---~~~~~-----------~~l~~ll~~~d~~vR~~ 73 (280)
T PRK09687 12 KEYSLYSQCKKLNDDELFRLLD----DHNSLKRISSIRVLQLRG---GQDVF-----------RLAIELCSSKNPIERDI 73 (280)
T ss_pred HHHHHHHHHhhccHHHHHHHHh----CCCHHHHHHHHHHHHhcC---cchHH-----------HHHHHHHhCCCHHHHHH
Confidence 3456788899999888888775 889999999888876553 22222 33556666777889999
Q ss_pred HHHHHHHhcccc
Q 005358 370 ANKVLSLLGEEQ 381 (700)
Q Consensus 370 A~KVL~lLg~~~ 381 (700)
|..+|..||...
T Consensus 74 A~~aLg~lg~~~ 85 (280)
T PRK09687 74 GADILSQLGMAK 85 (280)
T ss_pred HHHHHHhcCCCc
Confidence 999999998744
No 62
>PF12243 CTK3: CTD kinase subunit gamma CTK3
Probab=60.54 E-value=70 Score=31.40 Aligned_cols=95 Identities=15% Similarity=0.219 Sum_probs=58.8
Q ss_pred cCCCHHHH---HHHHHHHhhcCHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchh--HHHHHHHHHhhhHHHhhh
Q 005358 284 LQPTRDAI---QVFLVEAAKLDALAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEK--FSIILSYFCENNDVVVKC 358 (700)
Q Consensus 284 ~~PSreeL---q~Fl~~c~~Ld~e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~--~~~v~~Yf~eN~~~L~r~ 358 (700)
+.||.+.| ..|+=+|..+ .+.+..++.+.|++..--.|...++.||+|....-... ...+.++....-..|..+
T Consensus 17 L~aS~qSi~kaa~fAlk~~~~-~edL~~cIle~le~~~lN~R~nI~~fID~l~e~~~~~~~~~~~Yv~~l~~dL~~Iv~~ 95 (139)
T PF12243_consen 17 LNASQQSIQKAAQFALKNRDM-EEDLWSCILEQLEKENLNTRINIFYFIDSLCESSQKSKKYNYPYVSMLQRDLPRIVDA 95 (139)
T ss_pred cchhHHHHHHHHHHHHHcccc-HHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHhcccccchhHHHHHHHHHHHHHH
Confidence 45555544 5677777332 36677788888888888889999999999887653333 222334444444444444
Q ss_pred hcCCChh---HHHHHHHHHHHhcc
Q 005358 359 SESPQSS---LREKANKVLSLLGE 379 (700)
Q Consensus 359 ~~s~q~~---LReKA~KVL~lLg~ 379 (700)
+--+... =+.-+.|||+.|..
T Consensus 96 V~P~~~~g~~N~~~~~kvL~~~~~ 119 (139)
T PF12243_consen 96 VAPPDNSGAANLKSVRKVLKNWSK 119 (139)
T ss_pred hCCCCCccchHHHHHHHHHHHHHH
Confidence 4443332 34567778887754
No 63
>PF07923 N1221: N1221-like protein; InterPro: IPR012486 The sequences featured in this family are similar to a hypothetical protein product of ORF N1221 in the CPT1-SPC98 intergenic region of the yeast genome (P53917 from SWISSPROT). This encodes an acidic polypeptide with several possible transmembrane regions [].
Probab=60.14 E-value=18 Score=38.83 Aligned_cols=52 Identities=17% Similarity=0.187 Sum_probs=43.0
Q ss_pred HHHHHHHHhhccCCCchHHHHHHHHHHHHh------cCChhhHHHHHHhHHHHHHhhc
Q 005358 50 EVSDFILKRLEHKSPVVKQKALRLIKYSVG------KSGTDFRREMQRHSAVVRQLFH 101 (700)
Q Consensus 50 eI~dyLlkRL~~ks~hVKlKaLKILkyLc~------~Gs~~F~r~lrrns~~IK~l~~ 101 (700)
..+..|+..|.+..+.++++|||+|.|++. ...++-+.|+|+|...+.+|--
T Consensus 60 ~~i~~ll~~L~~~~~~~R~~al~~LlYi~~G~~~~~~s~~~ql~~i~~N~~lL~~~g~ 117 (293)
T PF07923_consen 60 DFIEKLLDQLESSDSEDRLEALRALLYIAQGTWGETASEEEQLQWIRRNVFLLYECGG 117 (293)
T ss_pred HHHHHHHHhccccchhhHHHHHHHHHHHHcCCccccCCHHHHHHHHHHHHHHHHHhhh
Confidence 566778889999998899999999999984 3457889999999987777543
No 64
>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=59.18 E-value=43 Score=28.91 Aligned_cols=71 Identities=18% Similarity=0.069 Sum_probs=50.9
Q ss_pred HHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHHHHHHHhhh-HHHhhhhcCCChhHHHHHHHHHHHhccc
Q 005358 306 MSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSIILSYFCENN-DVVVKCSESPQSSLREKANKVLSLLGEE 380 (700)
Q Consensus 306 V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~Yf~eN~-~~L~r~~~s~q~~LReKA~KVL~lLg~~ 380 (700)
+++.|.+.|.+..|.+|..++.+|..+..... . ....++..+. +.+..+.......+|..|-.+|..|-..
T Consensus 8 ~i~~l~~~l~~~~~~~~~~a~~~l~~l~~~~~--~--~~~~~~~~~~i~~l~~~l~~~~~~v~~~a~~~L~~l~~~ 79 (120)
T cd00020 8 GLPALVSLLSSSDENVQREAAWALSNLSAGNN--D--NIQAVVEAGGLPALVQLLKSEDEEVVKAALWALRNLAAG 79 (120)
T ss_pred ChHHHHHHHHcCCHHHHHHHHHHHHHHhcCCH--H--HHHHHHHCCChHHHHHHHhCCCHHHHHHHHHHHHHHccC
Confidence 55666677778889999999999999887532 1 1122223222 7777777778889999999999988543
No 65
>KOG1086 consensus Cytosolic sorting protein/ADP-ribosylation factor effector GGA [Intracellular trafficking, secretion, and vesicular transport]
Probab=57.32 E-value=53 Score=37.92 Aligned_cols=89 Identities=20% Similarity=0.192 Sum_probs=57.3
Q ss_pred HHHHHHHHHHhh--cCHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHHHHHHHhhhHHHhhhh------c
Q 005358 289 DAIQVFLVEAAK--LDALAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSIILSYFCENNDVVVKCS------E 360 (700)
Q Consensus 289 eeLq~Fl~~c~~--Ld~e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~Yf~eN~~~L~r~~------~ 360 (700)
+.|+-|++...+ -....-..+|..||+++....-+-||.|||.+++..+...++.|-.|--- .+|++.+ .
T Consensus 27 ~ai~~fceqinkdp~gp~lAv~LlaHKiqSPqe~EAl~altvLe~cmkncGekfH~evgkfrFL--NELIkvvsPKYlG~ 104 (594)
T KOG1086|consen 27 KAIDGFCEQINKDPEGPLLAVRLLAHKIQSPQEWEALQALTVLEYCMKNCGEKFHEEVGKFRFL--NELIKVVSPKYLGS 104 (594)
T ss_pred HHHHHHHHHHhcCCCCchhHHHHHHhhcCChhHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH--HHHHHHhCchhcch
Confidence 345556555554 11245667889999998888999999999999999998877777666432 2233322 1
Q ss_pred CCChhHHHHHHHHHHHhcc
Q 005358 361 SPQSSLREKANKVLSLLGE 379 (700)
Q Consensus 361 s~q~~LReKA~KVL~lLg~ 379 (700)
-.-..||.|..++|=-+..
T Consensus 105 ~tSekvKtkiIelLfsWtv 123 (594)
T KOG1086|consen 105 RTSEKVKTKIIELLFSWTV 123 (594)
T ss_pred hhhHHHHHHHHHHHhhhee
Confidence 1224466666665554444
No 66
>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=55.77 E-value=53 Score=28.33 Aligned_cols=69 Identities=20% Similarity=0.093 Sum_probs=50.1
Q ss_pred HHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHHHHHHHhh--hHHHhhhhcCCChhHHHHHHHHHHHhc
Q 005358 305 AMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSIILSYFCEN--NDVVVKCSESPQSSLREKANKVLSLLG 378 (700)
Q Consensus 305 ~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~Yf~eN--~~~L~r~~~s~q~~LReKA~KVL~lLg 378 (700)
.+++.|.+-|.+..+.++..|+.+|-.|..... ...+.+.++ ...|.++.......+|+.|..+|..|.
T Consensus 49 ~~i~~l~~~l~~~~~~v~~~a~~~L~~l~~~~~-----~~~~~~~~~g~l~~l~~~l~~~~~~~~~~a~~~l~~l~ 119 (120)
T cd00020 49 GGLPALVQLLKSEDEEVVKAALWALRNLAAGPE-----DNKLIVLEAGGVPKLVNLLDSSNEDIQKNATGALSNLA 119 (120)
T ss_pred CChHHHHHHHhCCCHHHHHHHHHHHHHHccCcH-----HHHHHHHHCCChHHHHHHHhcCCHHHHHHHHHHHHHhh
Confidence 445555555667889999999999999987542 123333333 477778888888999999999988763
No 67
>COG5098 Chromosome condensation complex Condensin, subunit D2 [Chromatin structure and dynamics / Cell division and chromosome partitioning]
Probab=55.67 E-value=32 Score=41.79 Aligned_cols=77 Identities=22% Similarity=0.078 Sum_probs=56.8
Q ss_pred HHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHHHHHHHhhhHHHhhhhcCCChhHHHHHHHHHHHhcccccC
Q 005358 304 LAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSIILSYFCENNDVVVKCSESPQSSLREKANKVLSLLGEEQAG 383 (700)
Q Consensus 304 e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~Yf~eN~~~L~r~~~s~q~~LReKA~KVL~lLg~~~~~ 383 (700)
..+..+|.+||++...-+|.|||-++|-|+.....-.- --.|-...+.||....-.-||.+|.|++..|=.--|=
T Consensus 345 ~~Lv~ll~ERl~D~~py~RtKalqv~~kifdl~sk~~~-----~r~ev~~lv~r~lqDrss~VRrnaikl~SkLL~~HPF 419 (1128)
T COG5098 345 NDLVGLLVERLSDTYPYTRTKALQVLEKIFDLNSKTVG-----RRHEVIRLVGRRLQDRSSVVRRNAIKLCSKLLMRHPF 419 (1128)
T ss_pred HHHHHHHHHHhhccchHHHHHHHHHHHHHHhCcccccc-----hHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhcCCh
Confidence 46788999999998888999999999999875532110 0122235677888888899999999999877654444
Q ss_pred Cc
Q 005358 384 GL 385 (700)
Q Consensus 384 ~~ 385 (700)
+.
T Consensus 420 ~~ 421 (1128)
T COG5098 420 AS 421 (1128)
T ss_pred hh
Confidence 33
No 68
>KOG3091 consensus Nuclear pore complex, p54 component (sc Nup57) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=55.49 E-value=73 Score=37.21 Aligned_cols=115 Identities=15% Similarity=0.180 Sum_probs=70.3
Q ss_pred HHHHHhhhhcccCCCCCCCchhhHHHHHHHHHhccch--hhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHH
Q 005358 10 SYWRSRMIDGATSDEDKVTPVYKLEEICELLRSSHVS--IGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRR 87 (700)
Q Consensus 10 ~~~~~~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s--~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r 87 (700)
-.||+.++++=-++.=+|.|.|=|+|+-+...--.+. ..+..|+.|..|+..-..|---=+-||++|= +.+.+.-+
T Consensus 313 ~~W~QA~~dnp~s~kliPVpvvGF~dL~~R~K~Q~q~~~~~r~ri~~i~e~v~eLqk~~ad~~~KI~~~k--~r~~~Ls~ 390 (508)
T KOG3091|consen 313 RIWRQAMKDNPPSNKLIPVPVVGFEDLRQRLKVQDQEVKQHRIRINAIGERVTELQKHHADAVAKIEEAK--NRHVELSH 390 (508)
T ss_pred HHHHHHhhcCCCcccccceeccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHH--HHHHHHHH
Confidence 4799999999899999999999999999887633211 1235677776666543322223345565552 22333333
Q ss_pred HHHHhHHHHHHhhcccCCCCCCCCchhhHHHHHHHHHHHHHhhc
Q 005358 88 EMQRHSAVVRQLFHYKGQLDPLKGDALNKAVRDMAHEAISAIFS 131 (700)
Q Consensus 88 ~lrrns~~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll~aLf~ 131 (700)
.+-|-.-.+..++++.++.+| | .+.+|++++.|+.-|-+
T Consensus 391 RiLRv~ikqeilr~~G~~L~~---~--EE~Lr~Kldtll~~ln~ 429 (508)
T KOG3091|consen 391 RILRVMIKQEILRKRGYALTP---D--EEELRAKLDTLLAQLNA 429 (508)
T ss_pred HHHHHHHHHHHHhccCCcCCc---c--HHHHHHHHHHHHHHhcC
Confidence 333333334445555555553 3 35799999988876644
No 69
>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=55.27 E-value=16 Score=26.23 Aligned_cols=30 Identities=23% Similarity=0.277 Sum_probs=25.5
Q ss_pred HHHHHHHhhccCCCchHHHHHHHHHHHHhc
Q 005358 51 VSDFILKRLEHKSPVVKQKALRLIKYSVGK 80 (700)
Q Consensus 51 I~dyLlkRL~~ks~hVKlKaLKILkyLc~~ 80 (700)
|+..|++-|+++++.|+.-|.+.|.-++++
T Consensus 1 llp~l~~~l~D~~~~VR~~a~~~l~~i~~~ 30 (31)
T PF02985_consen 1 LLPILLQLLNDPSPEVRQAAAECLGAIAEH 30 (31)
T ss_dssp HHHHHHHHHT-SSHHHHHHHHHHHHHHHHT
T ss_pred CHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Confidence 578899999999999999999999888764
No 70
>PF08167 RIX1: rRNA processing/ribosome biogenesis
Probab=54.20 E-value=53 Score=32.31 Aligned_cols=72 Identities=19% Similarity=0.195 Sum_probs=54.7
Q ss_pred hhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcC-ChhhHH----HHHHhHHHHHHhhcccCCCCCCCCchhhHHHHH
Q 005358 46 SIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKS-GTDFRR----EMQRHSAVVRQLFHYKGQLDPLKGDALNKAVRD 120 (700)
Q Consensus 46 s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~G-s~~F~r----~lrrns~~IK~l~~F~GppDpl~Gd~l~q~VR~ 120 (700)
+.+..+...|.+.|+++++.-+.+.+.+++-+|..+ .+-|.+ |++.-..+++. +|| ..+++
T Consensus 21 ~~l~~l~~ri~~LL~s~~~~~rw~G~~Ll~~~~~~~~~e~l~~~~~~W~~~Ll~~L~~-------~~~-------~~~~~ 86 (165)
T PF08167_consen 21 SALHKLVTRINSLLQSKSAYSRWAGLCLLKVTVEQCSWEILLSHGSQWLRALLSILEK-------PDP-------PSVLE 86 (165)
T ss_pred HHHHHHHHHHHHHhCCCChhhHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHcC-------CCC-------HHHHH
Confidence 346788899999999999999999999999999998 455534 44443333333 332 34889
Q ss_pred HHHHHHHHhhc
Q 005358 121 MAHEAISAIFS 131 (700)
Q Consensus 121 ~AkEll~aLf~ 131 (700)
.|-.++..||.
T Consensus 87 ~ai~~L~~l~~ 97 (165)
T PF08167_consen 87 AAIITLTRLFD 97 (165)
T ss_pred HHHHHHHHHHH
Confidence 99999999998
No 71
>PF07651 ANTH: ANTH domain; InterPro: IPR011417 AP180 is an endocytotic accessory protein that has been implicated in the formation of clathrin-coated pits. The domain is involved in phosphatidylinositol 4,5-bisphosphate binding and is a universal adaptor for nucleation of clathrin coats [, ].; GO: 0005543 phospholipid binding; PDB: 1HX8_A 3ZYM_A 1HFA_A 1HG2_A 3ZYL_B 3ZYK_A 1HG5_A 1HF8_A.
Probab=52.53 E-value=51 Score=34.44 Aligned_cols=68 Identities=21% Similarity=0.306 Sum_probs=47.8
Q ss_pred hHHHHHHHHhhcCCcccCCCHHHHHHHHHHHhh-cCHHHHHHHHHHHhCCc-hHHHHHHHHHHHHHHHhccCc
Q 005358 268 REEKLLETIVTYGGVRLQPTRDAIQVFLVEAAK-LDALAMSRALEAKLQSP-LWQVRMKAICVLESILRKKDD 338 (700)
Q Consensus 268 ~E~~LVe~i~T~gGvr~~PSreeLq~Fl~~c~~-Ld~e~V~elL~~kL~~~-~WQvrlRALcvIEaLl~s~~~ 338 (700)
.|..+++. |. ..-..|-..=++.-+..... .++..++.+|.+||... .|.|-+|+|.+|=.||+.+..
T Consensus 4 l~~av~KA--T~-~~~~ppk~Khv~~il~~t~~~~~~~~~~~~l~~Rl~~~~~w~V~~K~Lil~H~llr~G~~ 73 (280)
T PF07651_consen 4 LEKAVIKA--TS-HDEAPPKEKHVREILSATSSPESVAFLFWALSRRLPLTRNWIVALKALILLHRLLRDGHP 73 (280)
T ss_dssp HHHHHHHH--T--SSS---HHHHHHHHHHHCSTTS-HHHHHHHHHHHCTSS-SHHHHHHHHHHHHHHHHHS-C
T ss_pred HHHHHHHH--cC-CCCCCCCHHHHHHHHHHhcCCccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHcCch
Confidence 45555553 43 23344555556666666666 78899999999999776 999999999999999998764
No 72
>KOG2956 consensus CLIP-associating protein [General function prediction only]
Probab=51.81 E-value=71 Score=37.26 Aligned_cols=91 Identities=18% Similarity=0.258 Sum_probs=63.4
Q ss_pred hHHHHHHHHHhccc----hhhHHHHHHHHHhhcc-CCCchHHHHHHHHHHHHhcCChhhHHHHHHhHHHHHHhhcccCCC
Q 005358 32 KLEEICELLRSSHV----SIGKEVSDFILKRLEH-KSPVVKQKALRLIKYSVGKSGTDFRREMQRHSAVVRQLFHYKGQL 106 (700)
Q Consensus 32 l~~EIA~~t~~s~~----s~~~eI~dyLlkRL~~-ks~hVKlKaLKILkyLc~~Gs~~F~r~lrrns~~IK~l~~F~Gpp 106 (700)
.+.||-+|+.+... +...+|+.-|+.=|.+ ++..+|.=|||||.-+|.+-...|....-- ++-|.+-...
T Consensus 307 alsel~~m~~e~sfsvWeq~f~~iL~~l~EvL~d~~~~~~k~laLrvL~~ml~~Q~~~l~DstE~--ai~K~Leaa~--- 381 (516)
T KOG2956|consen 307 ALSELPKMLCEGSFSVWEQHFAEILLLLLEVLSDSEDEIIKKLALRVLREMLTNQPARLFDSTEI--AICKVLEAAK--- 381 (516)
T ss_pred HHHHHHHHHHccchhHHHHHHHHHHHHHHHHHccchhhHHHHHHHHHHHHHHHhchHhhhchHHH--HHHHHHHHHh---
Confidence 35567777765422 2234799999999998 778899999999999999988887754322 2223332222
Q ss_pred CCCCCchhhHHHHHHHHHHHHHhhcC
Q 005358 107 DPLKGDALNKAVRDMAHEAISAIFSE 132 (700)
Q Consensus 107 Dpl~Gd~l~q~VR~~AkEll~aLf~d 132 (700)
|...+-||.++++|+..|-+-
T Consensus 382 -----ds~~~v~~~Aeed~~~~las~ 402 (516)
T KOG2956|consen 382 -----DSQDEVMRVAEEDCLTTLASH 402 (516)
T ss_pred -----CCchhHHHHHHHHHHHHHHhh
Confidence 344556999999998888773
No 73
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=50.40 E-value=78 Score=36.24 Aligned_cols=94 Identities=15% Similarity=0.130 Sum_probs=63.7
Q ss_pred CHHHHHHHHHHHhhcCH-----HHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhH-HHHHHHHHhhhHHHhhhhc
Q 005358 287 TRDAIQVFLVEAAKLDA-----LAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKF-SIILSYFCENNDVVVKCSE 360 (700)
Q Consensus 287 SreeLq~Fl~~c~~Ld~-----e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~-~~v~~Yf~eN~~~L~r~~~ 360 (700)
+.|.-+-.+.-|-++.. ...+.+|.+||....--|.|+||.++.+++...+.... ++...=|. ..|.++.+
T Consensus 22 T~enW~~IlDvCD~v~~~~~~~kd~lk~i~KRln~~dphV~L~AlTLlda~~~NCg~~~r~EVsSr~F~---~el~al~~ 98 (462)
T KOG2199|consen 22 TSENWSLILDVCDKVGSDPDGGKDCLKAIMKRLNHKDPHVVLQALTLLDACVANCGKRFRLEVSSRDFT---TELRALIE 98 (462)
T ss_pred ccccHHHHHHHHHhhcCCCcccHHHHHHHHHHhcCCCcchHHHHHHHHHHHHHhcchHHHHHHhhhhHH---HHHHHHHh
Confidence 44555555555655432 56778888999766667999999999999987654322 23333333 45555444
Q ss_pred -CCChhHHHHHHHHHHHhcccccC
Q 005358 361 -SPQSSLREKANKVLSLLGEEQAG 383 (700)
Q Consensus 361 -s~q~~LReKA~KVL~lLg~~~~~ 383 (700)
+.|..|++|-+-+++.|-.+.-+
T Consensus 99 ~~~h~kV~~k~~~lv~eWsee~K~ 122 (462)
T KOG2199|consen 99 SKAHPKVCEKMRDLVKEWSEEFKK 122 (462)
T ss_pred hcccHHHHHHHHHHHHHHHHHhcc
Confidence 89999999999998888764433
No 74
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=49.66 E-value=53 Score=31.90 Aligned_cols=61 Identities=23% Similarity=0.219 Sum_probs=50.5
Q ss_pred HHHHhhcCCcccCCCHHHHHHHHHHHhh-cCHHHHHHHHHHHhCCchHHHHHHHHHHHHHHH
Q 005358 273 LETIVTYGGVRLQPTRDAIQVFLVEAAK-LDALAMSRALEAKLQSPLWQVRMKAICVLESIL 333 (700)
Q Consensus 273 Ve~i~T~gGvr~~PSreeLq~Fl~~c~~-Ld~e~V~elL~~kL~~~~WQvrlRALcvIEaLl 333 (700)
+.+++..-|.|++|+|..|-.++.+... +.++.|.+.|.+....-+--+.+|+|-.++.+.
T Consensus 8 ~~~~lk~~glr~T~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~G 69 (145)
T COG0735 8 AIERLKEAGLRLTPQRLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAG 69 (145)
T ss_pred HHHHHHHcCCCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCC
Confidence 4455666799999999999999998855 999999999999877777788899997776543
No 75
>COG4396 Mu-like prophage host-nuclease inhibitor protein Gam [General function prediction only]
Probab=47.17 E-value=54 Score=32.57 Aligned_cols=66 Identities=11% Similarity=0.233 Sum_probs=48.9
Q ss_pred cCCCHHHHHHHHHHHhhcCHH--HHHHHHHHHhC--CchHHHHHHHHHH-HHHHHhccCchhHHHHHHHHHhhhHHHhh
Q 005358 284 LQPTRDAIQVFLVEAAKLDAL--AMSRALEAKLQ--SPLWQVRMKAICV-LESILRKKDDEKFSIILSYFCENNDVVVK 357 (700)
Q Consensus 284 ~~PSreeLq~Fl~~c~~Ld~e--~V~elL~~kL~--~~~WQvrlRALcv-IEaLl~s~~~d~~~~v~~Yf~eN~~~L~r 357 (700)
.+.++++++.|++....|.-+ ++--...+|.- +..+--+++.||. |+.|.+ .|.+|-..|.+.|-.
T Consensus 13 a~q~~eeV~~~Ir~iGDlqRE~~RLeTemnDk~aai~e~Yapq~~~lk~EI~~L~k--------~vq~yCeanrDELTe 83 (170)
T COG4396 13 AAQDKEEVTAFIRQIGDLQREVKRLETEMNDKKAAIEEEYAPQAAPLKAEIMSLTK--------RVQAYCEANRDELTE 83 (170)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHhcchHhHHHHHhhhhhHHHHHHHHHHHH--------HHHHHHHhCHHHHhc
Confidence 566899999999999988765 34444455542 4566778888988 787775 577888888888764
No 76
>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=46.49 E-value=1.8e+02 Score=29.99 Aligned_cols=114 Identities=14% Similarity=0.107 Sum_probs=71.9
Q ss_pred HHhhhhcccCCCCCCCchhhHHHHHHHHHh-ccchhhH----HHHHHHHHhhccCCCchHHHHHHHHHHHHhcC---Chh
Q 005358 13 RSRMIDGATSDEDKVTPVYKLEEICELLRS-SHVSIGK----EVSDFILKRLEHKSPVVKQKALRLIKYSVGKS---GTD 84 (700)
Q Consensus 13 ~~~lV~kATSddd~PtPGYl~~EIA~~t~~-s~~s~~~----eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~G---s~~ 84 (700)
..+++-..-...+.|--....+-+-++... .. +.+- .|+--|-+-|+.+++.|+..+|++|..||.-+ .+.
T Consensus 39 ~Lpif~dGL~Et~~Py~flA~~g~~dll~~~~~-~kilPvlPqLI~plk~AL~tr~~~V~~~~L~~Lq~Lv~~~~~vG~a 117 (183)
T PF10274_consen 39 YLPIFFDGLRETEHPYRFLARQGIKDLLERGGG-EKILPVLPQLIIPLKRALNTRDPEVFCATLKALQQLVTSSDMVGEA 117 (183)
T ss_pred HHHHHHhhhhccCccHHHHHHHHHHHHHHhcch-hHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhhhhhhHH
Confidence 346666777778888777777777777765 32 2222 34555667888999999999999999996532 344
Q ss_pred hHHHHHHhHHHHHHhhcccCCCCCCCCc----hhhHHHHHHHHHHHHHhhc
Q 005358 85 FRREMQRHSAVVRQLFHYKGQLDPLKGD----ALNKAVRDMAHEAISAIFS 131 (700)
Q Consensus 85 F~r~lrrns~~IK~l~~F~GppDpl~Gd----~l~q~VR~~AkEll~aLf~ 131 (700)
.+-.+|+-..++...++-+ . -.|| .-.+.+++..+|.+++|=-
T Consensus 118 LvPyyrqLLp~ln~f~~k~---~-n~gd~i~y~~~~~~~dlI~etL~~lE~ 164 (183)
T PF10274_consen 118 LVPYYRQLLPVLNLFKNKN---V-NLGDGIDYRKRKNLGDLIQETLELLER 164 (183)
T ss_pred HHHHHHHHHHHHHHHHhcc---c-CCCcccccccccchhHHHHHHHHHHHH
Confidence 4444444444433322222 1 1233 2345688888888888754
No 77
>KOG0414 consensus Chromosome condensation complex Condensin, subunit D2 [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]
Probab=45.26 E-value=45 Score=42.42 Aligned_cols=36 Identities=19% Similarity=0.316 Sum_probs=32.0
Q ss_pred HHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhh
Q 005358 50 EVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDF 85 (700)
Q Consensus 50 eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F 85 (700)
++++.|..||-+-++||+.|||.|..+||..-+...
T Consensus 359 ~~le~l~erl~Dvsa~vRskVLqv~~~l~~~~s~p~ 394 (1251)
T KOG0414|consen 359 ELLELLRERLLDVSAYVRSKVLQVFRRLFQQHSIPL 394 (1251)
T ss_pred HHHHHHHHHhhcccHHHHHHHHHHHHHHHHccCCCc
Confidence 489999999999999999999999999998765433
No 78
>KOG2025 consensus Chromosome condensation complex Condensin, subunit G [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]
Probab=43.69 E-value=34 Score=41.53 Aligned_cols=41 Identities=15% Similarity=0.233 Sum_probs=34.1
Q ss_pred chhhHHHHHHHHHhhccCCCchHHHHHHHHHHHH-hcCChhh
Q 005358 45 VSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSV-GKSGTDF 85 (700)
Q Consensus 45 ~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc-~~Gs~~F 85 (700)
.+..+.|.+.|+.||.++.|.|+..|+.+|-++- ..+.++|
T Consensus 121 d~vfn~l~e~l~~Rl~Drep~VRiqAv~aLsrlQ~d~~dee~ 162 (892)
T KOG2025|consen 121 DDVFNKLNEKLLIRLKDREPNVRIQAVLALSRLQGDPKDEEC 162 (892)
T ss_pred HHHHHHHHHHHHHHHhccCchHHHHHHHHHHHHhcCCCCCcc
Confidence 3566789999999999999999999999999987 4445544
No 79
>PF04003 Utp12: Dip2/Utp12 Family; InterPro: IPR007148 A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA - the small-subunit (SSU) processome [, ]. This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties: They are nucleolar. They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome). They are required for 18S rRNA biogenesis. There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble []. From electron microscopy the SSU processome may correspond to the terminal knobs visualized at the 5' ends of nascent 18S rRNA. This domain is found at the C terminus of proteins containing WD40 repeats. These proteins are part of the U3 ribonucleoprotein. In yeast, these proteins are called Utp5, Utp1 or Pwp2, Utp12 or DIP2 Q12220 from SWISSPROT. They interact with snoRNA U3 and with MPP10 []. Pwp2 is an essential Saccharomyces cerevisiae (Baker's yeast) protein involved in cell separation.
Probab=43.24 E-value=1.9e+02 Score=25.89 Aligned_cols=45 Identities=31% Similarity=0.410 Sum_probs=34.1
Q ss_pred HHHHHHHHhccchhhHHHHHHHHHhhc-cCCCchHHHHHHHHHHHHh
Q 005358 34 EEICELLRSSHVSIGKEVSDFILKRLE-HKSPVVKQKALRLIKYSVG 79 (700)
Q Consensus 34 ~EIA~~t~~s~~s~~~eI~dyLlkRL~-~ks~hVKlKaLKILkyLc~ 79 (700)
++|......=+.+.+..++++|..+++ .+++|| -=.|+.|++++.
T Consensus 16 ~~I~~tv~~Lp~~~~~~LL~~l~~~l~~~~~~~~-e~~l~Wl~~ll~ 61 (110)
T PF04003_consen 16 SDIENTVRSLPFSYAERLLQFLSERLQTRKSPHV-EFLLRWLKALLK 61 (110)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHHHhcccCCCch-hHHHHHHHHHHH
Confidence 344444444455567799999999999 888998 567899999885
No 80
>KOG2160 consensus Armadillo/beta-catenin-like repeat-containing protein [Posttranslational modification, protein turnover, chaperones]
Probab=42.81 E-value=1.4e+02 Score=33.42 Aligned_cols=59 Identities=27% Similarity=0.284 Sum_probs=44.1
Q ss_pred CCchHHHHHHHHHHHHHHHhccCchhHHHHHHHHHhhh-HHHhhhhcC--CChhHHHHHHHHHHHh
Q 005358 315 QSPLWQVRMKAICVLESILRKKDDEKFSIILSYFCENN-DVVVKCSES--PQSSLREKANKVLSLL 377 (700)
Q Consensus 315 ~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~Yf~eN~-~~L~r~~~s--~q~~LReKA~KVL~lL 377 (700)
.+.+--+|-|||++|-+|++..-. ...+|++.|. ..|+++.++ ....++.||.-+|..|
T Consensus 177 ~~~~~~~r~kaL~AissLIRn~~~----g~~~fl~~~G~~~L~~vl~~~~~~~~lkrK~~~Ll~~L 238 (342)
T KOG2160|consen 177 SDDPNTVRTKALFAISSLIRNNKP----GQDEFLKLNGYQVLRDVLQSNNTSVKLKRKALFLLSLL 238 (342)
T ss_pred cCCCchHHHHHHHHHHHHHhcCcH----HHHHHHhcCCHHHHHHHHHcCCcchHHHHHHHHHHHHH
Confidence 578888999999999999996531 4567888887 778888888 4555666666655554
No 81
>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=42.49 E-value=89 Score=30.23 Aligned_cols=55 Identities=18% Similarity=0.202 Sum_probs=37.0
Q ss_pred hHHHHHHHHHHHHhcCChhhHHHHHHhHHHHHHhhcccCCCCCCCCchhhHHHHHHHHHHHHHhh
Q 005358 66 VKQKALRLIKYSVGKSGTDFRREMQRHSAVVRQLFHYKGQLDPLKGDALNKAVRDMAHEAISAIF 130 (700)
Q Consensus 66 VKlKaLKILkyLc~~Gs~~F~r~lrrns~~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll~aLf 130 (700)
+-+.+||+||.|+.+.. . +..+-++...|..+...-.. .+-.+|..|-|++.+|.
T Consensus 132 ~~~~~l~Clkal~n~~~-G-~~~v~~~~~~v~~i~~~L~s--------~~~~~r~~~leiL~~lc 186 (187)
T PF06371_consen 132 IEHECLRCLKALMNTKY-G-LEAVLSHPDSVNLIALSLDS--------PNIKTRKLALEILAALC 186 (187)
T ss_dssp HHHHHHHHHHHHTSSHH-H-HHHHHCSSSHHHHHHHT--T--------TSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHccHH-H-HHHHHcCcHHHHHHHHHHCC--------CCHHHHHHHHHHHHHHH
Confidence 55789999999997552 2 34444466666666555433 23469999999998874
No 82
>smart00582 RPR domain present in proteins, which are involved in regulation of nuclear pre-mRNA.
Probab=41.74 E-value=1.6e+02 Score=26.89 Aligned_cols=88 Identities=16% Similarity=0.196 Sum_probs=56.1
Q ss_pred chhhHHHHHHHHHhccchhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCCh----hhHHHHHHhHH-HHHHhhccc
Q 005358 29 PVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGT----DFRREMQRHSA-VVRQLFHYK 103 (700)
Q Consensus 29 PGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~----~F~r~lrrns~-~IK~l~~F~ 103 (700)
..-...++..++.+.. +...+|++.|.+++.+..+.-|+-.|=|+..++++... .|+..+..... +.+.+....
T Consensus 12 s~~~I~~lt~~~~~~~-~~a~~Iv~~i~~~~~~~~~~~kL~~LYlindIl~n~~~~~~~~f~~~~~~~~~~~~~~~~~~~ 90 (121)
T smart00582 12 SQESIQTLTKWAIEHA-SHAKEIVELWEKYIKKAPPPRKLPLLYLLDSIVQNSKRKYGSEFGDELGPVFQDALRDVLGAA 90 (121)
T ss_pred cHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHhCCccceehhHHhHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHhC
Confidence 3344566666666543 35579999999999988888888888888888776643 45554444432 222222111
Q ss_pred CCCCCCCCchhhHHHHHHHHHHHHH
Q 005358 104 GQLDPLKGDALNKAVRDMAHEAISA 128 (700)
Q Consensus 104 GppDpl~Gd~l~q~VR~~AkEll~a 128 (700)
...+|.+...++++
T Consensus 91 -----------~~~~~~ki~kll~i 104 (121)
T smart00582 91 -----------NDETKKKIRRLLNI 104 (121)
T ss_pred -----------CHHHHHHHHHHHHH
Confidence 14578777777765
No 83
>PRK13800 putative oxidoreductase/HEAT repeat-containing protein; Provisional
Probab=40.93 E-value=61 Score=40.08 Aligned_cols=21 Identities=14% Similarity=0.297 Sum_probs=10.5
Q ss_pred HhhhhcCCChhHHHHHHHHHH
Q 005358 355 VVKCSESPQSSLREKANKVLS 375 (700)
Q Consensus 355 L~r~~~s~q~~LReKA~KVL~ 375 (700)
|.++.+.....||..|.+-|+
T Consensus 875 L~~al~D~d~~Vr~~A~~aL~ 895 (897)
T PRK13800 875 LTTALTDSDADVRAYARRALA 895 (897)
T ss_pred HHHHHhCCCHHHHHHHHHHHh
Confidence 334444445555555555543
No 84
>PTZ00429 beta-adaptin; Provisional
Probab=39.18 E-value=8.4e+02 Score=30.22 Aligned_cols=72 Identities=11% Similarity=0.164 Sum_probs=42.7
Q ss_pred CHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHHHHHHHhhhHHHhhh-hcCCChhHHHHHHHHHHHhccc
Q 005358 302 DALAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSIILSYFCENNDVVVKC-SESPQSSLREKANKVLSLLGEE 380 (700)
Q Consensus 302 d~e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~Yf~eN~~~L~r~-~~s~q~~LReKA~KVL~lLg~~ 380 (700)
|+..+++.+.+.+....-.||+-.|.++--|+-..-.+....+ ...|..| ..+...-||+||.-..++|...
T Consensus 475 ~a~~~L~~~i~~f~~E~~~VqlqlLta~vKlfl~~p~~~~~~l-------~~vL~~~t~~~~d~DVRDRA~~Y~rLLs~~ 547 (746)
T PTZ00429 475 NGKDIIQRFIDTIMEHEQRVQLAILSAAVKMFLRDPQGMEPQL-------NRVLETVTTHSDDPDVRDRAFAYWRLLSKG 547 (746)
T ss_pred hHHHHHHHHHhhhccCCHHHHHHHHHHHHHHHhcCcHHHHHHH-------HHHHHHHHhcCCChhHHHHHHHHHHHHcCC
Confidence 5556665555555445557888887666655544322111111 1334445 3456678999999999999754
No 85
>PF01431 Peptidase_M13: Peptidase family M13 This is family M13 in the peptidase classification. ; InterPro: IPR018497 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M13 (neprilysin family, clan MA(E)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH []. M13 peptidases are well-studied proteases found in a wide range of organisms including mammals and bacteria. In mammals they participate in processes such as cardiovascular development, blood-pressure regulation, nervous control of respiration, and regulation of the function of neuropeptides in the central nervous system. In bacteria they may be used for digestion of milk [, ]. The family includes eukaryotic and prokaryotic oligopeptidases, as well as some of the proteins responsible for the molecular basis of the blood group antigens e.g. Kell []. Neprilysin (3.4.24.11 from EC), is another member of this group, it is variously known as common acute lymphoblastic leukemia antigen (CALLA), enkephalinase (gp100) and neutral endopeptidase metalloendopeptidase (NEP). It is a plasma membrane-bound mammalian enzyme that is able to digest biologically-active peptides, including enkephalins []. The zinc ligands of neprilysin are known and are analogous to those in thermolysin, a related peptidase [, ]. Neprilysins, like thermolysin, are inhibited by phosphoramidon, which appears to selectively inhibit this family in mammals. The enzymes are all oligopeptidases, digesting oligo- and polypeptides, but not proteins []. Neprilysin consists of a short cytoplasmic domain, a membrane-spanning region and a large extracellular domain. The cytoplasmic domain contains a conformationally-restrained octapeptide, which is thought to act as a stop transfer sequence that prevents proteolysis and secretion [, ].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2QPJ_A 1R1I_A 1R1J_A 1Y8J_A 1R1H_A 1DMT_A 2YB9_A 3DWB_A 3ZUK_A.
Probab=39.13 E-value=8.4 Score=38.38 Aligned_cols=28 Identities=32% Similarity=0.679 Sum_probs=19.3
Q ss_pred CCCccccCCCCCC---CCCchhHHHhHHHHH
Q 005358 600 IPAGMTLNPSIAS---QPMNYSAMGNLFAQQ 627 (700)
Q Consensus 600 ~~~~~~~~~~~~~---~~~~~~~~~~~~~~~ 627 (700)
||+|||.=|=|.. ..+|||.||.+||++
T Consensus 13 ip~~~l~~P~f~~~~p~~~~yg~lG~ilahe 43 (206)
T PF01431_consen 13 IPAGILQPPFFDPNYPPALNYGGLGFILAHE 43 (206)
T ss_dssp EEGGGSSTTT--TTS-HHHHHHTHHHHHHHH
T ss_pred ecHHHhCCccCCCCCCHHHHHHHHHHHHHHH
Confidence 5666644443332 679999999999987
No 86
>KOG0915 consensus Uncharacterized conserved protein [Function unknown]
Probab=38.51 E-value=78 Score=41.50 Aligned_cols=105 Identities=18% Similarity=0.190 Sum_probs=71.0
Q ss_pred HHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHHHHHHHhhhHHHhhhhcCCChhHHHHHHHHHHHhcccccCC
Q 005358 305 AMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSIILSYFCENNDVVVKCSESPQSSLREKANKVLSLLGEEQAGG 384 (700)
Q Consensus 305 ~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~Yf~eN~~~L~r~~~s~q~~LReKA~KVL~lLg~~~~~~ 384 (700)
.|+..|..-|-+..|+||--+=.++--|++.+..|.+ .+-..|-=+.+-|-++..+.+||+.|+|..+-|.=--...
T Consensus 1039 eIl~eLL~~lt~kewRVReasclAL~dLl~g~~~~~~---~e~lpelw~~~fRvmDDIKEsVR~aa~~~~~~lsKl~vr~ 1115 (1702)
T KOG0915|consen 1039 EILDELLVNLTSKEWRVREASCLALADLLQGRPFDQV---KEKLPELWEAAFRVMDDIKESVREAADKAARALSKLCVRI 1115 (1702)
T ss_pred HHHHHHHHhccchhHHHHHHHHHHHHHHHcCCChHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 4566677777899999999998899999999876654 2222333345778899999999998887766665322221
Q ss_pred cccCCcccccccccccccCCCccccCCCCC
Q 005358 385 LVSGSERSVKAETTTVVQMPDLIDTADPED 414 (700)
Q Consensus 385 ~~~~se~~vk~e~~~vvq~~DLId~g~~dd 414 (700)
-- +...++...+-.+-+|=|||.|-..+
T Consensus 1116 ~d--~~~~~~~~~~l~~iLPfLl~~gims~ 1143 (1702)
T KOG0915|consen 1116 CD--VTNGAKGKEALDIILPFLLDEGIMSK 1143 (1702)
T ss_pred cc--cCCcccHHHHHHHHHHHHhccCcccc
Confidence 10 11223444556677888998877643
No 87
>PRK09687 putative lyase; Provisional
Probab=38.15 E-value=95 Score=33.24 Aligned_cols=26 Identities=12% Similarity=0.374 Sum_probs=20.7
Q ss_pred HHHHHHHhhccCCCchHHHHHHHHHH
Q 005358 51 VSDFILKRLEHKSPVVKQKALRLIKY 76 (700)
Q Consensus 51 I~dyLlkRL~~ks~hVKlKaLKILky 76 (700)
-++.|.+.|.+.+..|+..+++.|..
T Consensus 24 ~~~~L~~~L~d~d~~vR~~A~~aL~~ 49 (280)
T PRK09687 24 NDDELFRLLDDHNSLKRISSIRVLQL 49 (280)
T ss_pred cHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 45778888899999998888877654
No 88
>KOG0980 consensus Actin-binding protein SLA2/Huntingtin-interacting protein Hip1 [Cytoskeleton]
Probab=36.60 E-value=1e+02 Score=38.47 Aligned_cols=110 Identities=15% Similarity=0.118 Sum_probs=81.8
Q ss_pred HHhhhhcccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhc-cCCCchHHHHHHHHHHHHhcCChhhHHHHHH
Q 005358 13 RSRMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLE-HKSPVVKQKALRLIKYSVGKSGTDFRREMQR 91 (700)
Q Consensus 13 ~~~lV~kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~-~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrr 91 (700)
...-|+||++-++.|+=-==.+-|.=.|++-.. -.+.=...+|+. .+++..-.|.+-+|--+++.||+....+.+|
T Consensus 7 q~~av~KAis~~Et~~K~KH~Rt~I~gTh~eks---a~~FWt~ik~~PL~~~~VltwKfchllHKvLreGHpsal~es~r 83 (980)
T KOG0980|consen 7 QLEAVQKAISKDETPPKRKHVRTIIVGTHDEKS---SKIFWTTIKRQPLENHEVLTWKFCHLLHKVLREGHPSALEESQR 83 (980)
T ss_pred HHHHHHHHhccccCCCchhhhhheeeeeccccc---chhHHHHhhccccccchHHHHHHHHHHHHHHHcCCcchhHHHHH
Confidence 456789999999988765444555444443221 244456778888 5667788999999999999999999999999
Q ss_pred hHHHHHHhhcccCCCCCCCCchhhHHHHHHHHHHHHHh
Q 005358 92 HSAVVRQLFHYKGQLDPLKGDALNKAVRDMAHEAISAI 129 (700)
Q Consensus 92 ns~~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEll~aL 129 (700)
+-.-|++|-.+-|.-. ++.+..||..-|=|..-|
T Consensus 84 ~r~~i~~l~r~w~~ls----~~Yg~lI~~Y~klL~~Kl 117 (980)
T KOG0980|consen 84 YKKWITQLGRMWGHLS----DGYGPLIRAYVKLLHDKL 117 (980)
T ss_pred HHHHHHHHHHHhcccc----ccchHHHHHHHHHHHHHH
Confidence 9999999977666332 456677999888776544
No 89
>PF11841 DUF3361: Domain of unknown function (DUF3361)
Probab=35.32 E-value=78 Score=31.87 Aligned_cols=46 Identities=22% Similarity=0.244 Sum_probs=37.5
Q ss_pred HHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHHHHHHH
Q 005358 304 LAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSIILSYFC 349 (700)
Q Consensus 304 e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~Yf~ 349 (700)
|.=++-|..+|+..+-+++.+|+.+|=||+.+.+++.-+.+.+++.
T Consensus 101 evt~~~Li~hLq~~~~~iq~naiaLinAL~~kA~~~~r~~i~~~l~ 146 (160)
T PF11841_consen 101 EVTLESLIRHLQVSNQEIQTNAIALINALFLKADDSKRKEIAETLS 146 (160)
T ss_pred cCCHHHHHHHHHcCCHHHHHHHHHHHHHHHhcCChHHHHHHHHHHH
Confidence 4445667777878999999999999999999998777667777774
No 90
>KOG4380 consensus Carnitine deficiency associated protein [General function prediction only]
Probab=35.24 E-value=51 Score=34.25 Aligned_cols=76 Identities=17% Similarity=0.143 Sum_probs=43.1
Q ss_pred HHHHHHHHHHhCCchHHHHHHHHHHH--HHHHhccCchhHHHHHHHHHhhhHHHh--hhhcCCChhHHHHHHHHHHHhcc
Q 005358 304 LAMSRALEAKLQSPLWQVRMKAICVL--ESILRKKDDEKFSIILSYFCENNDVVV--KCSESPQSSLREKANKVLSLLGE 379 (700)
Q Consensus 304 e~V~elL~~kL~~~~WQvrlRALcvI--EaLl~s~~~d~~~~v~~Yf~eN~~~L~--r~~~s~q~~LReKA~KVL~lLg~ 379 (700)
.++|.+|.=. ..+...|-|||.|.+ |.|.+-..-+..+.+ ..|...|. -++..+...+-.-|-+|||||.+
T Consensus 135 ~AL~~iL~I~-~H~D~~VmmKA~~i~i~E~L~~D~iA~~~~~~----~~~~~~L~~~I~~~~~~~~~~~~sA~iLRLi~i 209 (244)
T KOG4380|consen 135 MALANLLQIQ-RHDDYLVMLKAIRILVQERLTQDAVAKANQTK----EGLPVALDKHILGFDTGDAVLNEAAQILRLLHI 209 (244)
T ss_pred HHHHHHhccc-cCCCHHHHHHHHHHHHHHHhhhHHHHHhHHHH----hcCcceecccccccCCcchHHHHHHHHHHHHHH
Confidence 4556555433 577888889988764 544432111111111 11111111 14566777788889999999998
Q ss_pred cccCC
Q 005358 380 EQAGG 384 (700)
Q Consensus 380 ~~~~~ 384 (700)
.+.--
T Consensus 210 ~~LR~ 214 (244)
T KOG4380|consen 210 EELRE 214 (244)
T ss_pred HHHHH
Confidence 76543
No 91
>PRK09462 fur ferric uptake regulator; Provisional
Probab=34.40 E-value=95 Score=29.80 Aligned_cols=56 Identities=13% Similarity=0.100 Sum_probs=45.9
Q ss_pred hhcCCcccCCCHHHHHHHHHHH--hhcCHHHHHHHHHHHhCCchHHHHHHHHHHHHHH
Q 005358 277 VTYGGVRLQPTRDAIQVFLVEA--AKLDALAMSRALEAKLQSPLWQVRMKAICVLESI 332 (700)
Q Consensus 277 ~T~gGvr~~PSreeLq~Fl~~c--~~Ld~e~V~elL~~kL~~~~WQvrlRALcvIEaL 332 (700)
+..-|.|++|.|..|-.++... .-+.++.|.+.|.++...-.--+-+|+|-.|+..
T Consensus 8 l~~~glr~T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~ 65 (148)
T PRK09462 8 LKKAGLKVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDA 65 (148)
T ss_pred HHHcCCCCCHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHC
Confidence 4445999999999999999975 3799999999999887666667889998776543
No 92
>PRK13800 putative oxidoreductase/HEAT repeat-containing protein; Provisional
Probab=34.13 E-value=73 Score=39.44 Aligned_cols=59 Identities=24% Similarity=0.244 Sum_probs=39.2
Q ss_pred HHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHHHHHHHhhhHHHhhhhcCCChhHHHHHHHHHHHhc
Q 005358 306 MSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSIILSYFCENNDVVVKCSESPQSSLREKANKVLSLLG 378 (700)
Q Consensus 306 V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~Yf~eN~~~L~r~~~s~q~~LReKA~KVL~lLg 378 (700)
+...|..-|.++.|+||..|+-+|..|-.. +. -..|..+-..+...||..|.+.|..|.
T Consensus 808 ~~~~l~~aL~d~d~~VR~~Aa~aL~~l~~~---~a-----------~~~L~~~L~D~~~~VR~~A~~aL~~~~ 866 (897)
T PRK13800 808 DVAAATAALRASAWQVRQGAARALAGAAAD---VA-----------VPALVEALTDPHLDVRKAAVLALTRWP 866 (897)
T ss_pred hHHHHHHHhcCCChHHHHHHHHHHHhcccc---ch-----------HHHHHHHhcCCCHHHHHHHHHHHhccC
Confidence 334555666677777777766666544321 11 155667777888999999999998873
No 93
>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=33.63 E-value=17 Score=28.59 Aligned_cols=29 Identities=14% Similarity=0.099 Sum_probs=24.9
Q ss_pred hhHHHHHHHHHhhccCCCchHHHHHHHHH
Q 005358 47 IGKEVSDFILKRLEHKSPVVKQKALRLIK 75 (700)
Q Consensus 47 ~~~eI~dyLlkRL~~ks~hVKlKaLKILk 75 (700)
...+++..|.+.|++.++.|+.+|...|-
T Consensus 25 ~~~~~~~~L~~~L~d~~~~VR~~A~~aLg 53 (55)
T PF13513_consen 25 YLPELLPALIPLLQDDDDSVRAAAAWALG 53 (55)
T ss_dssp HHHHHHHHHHHHTTSSSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 45689999999999999999999987764
No 94
>PF12169 DNA_pol3_gamma3: DNA polymerase III subunits gamma and tau domain III; InterPro: IPR022754 This domain is found in bacteria and eukaryotes, and is approximately 110 amino acids in length. It is found in association with PF00004 from PFAM. This domain is also present in the tau subunit before it undergoes cleavage. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. ; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G.
Probab=33.11 E-value=2.2e+02 Score=26.53 Aligned_cols=66 Identities=24% Similarity=0.243 Sum_probs=36.2
Q ss_pred HHHHHHHHhccchhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHHHHHHhHHHHHHhhcccCCCC
Q 005358 34 EEICELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREMQRHSAVVRQLFHYKGQLD 107 (700)
Q Consensus 34 ~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrrns~~IK~l~~F~GppD 107 (700)
+++.+++=--..+.+.++++.|.+ +. ..|+|+++.-++..| .++.+.++.-...+|.+.-++..++
T Consensus 4 e~V~~~lG~v~~~~i~~l~~ai~~---~d----~~~~l~~~~~l~~~G-~d~~~~l~~L~~~~R~ll~~k~~~~ 69 (143)
T PF12169_consen 4 EDVREILGLVDEEQIFELLDAILE---GD----AAEALELLNELLEQG-KDPKQFLDDLIEYLRDLLLYKITGD 69 (143)
T ss_dssp HHHHHHHTHTSTHHHHHHHHHHHT---T-----HHHHHHHHHHHHHCT---HHHHHHHHHHHHHHHHHHTTSGG
T ss_pred HHHHHHHCCCCHHHHHHHHHHHHc---CC----HHHHHHHHHHHHHhC-CCHHHHHHHHHHHHHHHHHHHhCCc
Confidence 444455432222334455555532 22 379999999999988 3444445555555666555555543
No 95
>PTZ00429 beta-adaptin; Provisional
Probab=32.54 E-value=1.9e+02 Score=35.66 Aligned_cols=85 Identities=15% Similarity=0.229 Sum_probs=57.7
Q ss_pred hhhHHHHHHHHHhccchhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHHHHHHhHHHHHHhhcccCCCCCC
Q 005358 30 VYKLEEICELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREMQRHSAVVRQLFHYKGQLDPL 109 (700)
Q Consensus 30 GYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrrns~~IK~l~~F~GppDpl 109 (700)
.|++.|.++..- .+.++++.+.+++...++.||+=.|...-.|.-+-.++.+..++ .+++.|+++.-.||
T Consensus 463 iWILGEy~~~I~-----~a~~~L~~~i~~f~~E~~~VqlqlLta~vKlfl~~p~~~~~~l~---~vL~~~t~~~~d~D-- 532 (746)
T PTZ00429 463 LWMLGEYCDFIE-----NGKDIIQRFIDTIMEHEQRVQLAILSAAVKMFLRDPQGMEPQLN---RVLETVTTHSDDPD-- 532 (746)
T ss_pred HHHHHhhHhhHh-----hHHHHHHHHHhhhccCCHHHHHHHHHHHHHHHhcCcHHHHHHHH---HHHHHHHhcCCChh--
Confidence 567777666432 24567766778888888899998888777665555555544332 35667777654333
Q ss_pred CCchhhHHHHHHHHHHHHHhhcC
Q 005358 110 KGDALNKAVRDMAHEAISAIFSE 132 (700)
Q Consensus 110 ~Gd~l~q~VR~~AkEll~aLf~d 132 (700)
||++|...+.+|-.+
T Consensus 533 --------VRDRA~~Y~rLLs~~ 547 (746)
T PTZ00429 533 --------VRDRAFAYWRLLSKG 547 (746)
T ss_pred --------HHHHHHHHHHHHcCC
Confidence 999999999988664
No 96
>PF12830 Nipped-B_C: Sister chromatid cohesion C-terminus
Probab=29.95 E-value=1.7e+02 Score=29.41 Aligned_cols=69 Identities=13% Similarity=0.174 Sum_probs=49.3
Q ss_pred hHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcC--ChhhHHHHHHhHHHHHHhhcccCCCCCCCCchhhHHHHHHHHHH
Q 005358 48 GKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKS--GTDFRREMQRHSAVVRQLFHYKGQLDPLKGDALNKAVRDMAHEA 125 (700)
Q Consensus 48 ~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~G--s~~F~r~lrrns~~IK~l~~F~GppDpl~Gd~l~q~VR~~AkEl 125 (700)
++.-++.+++-.-+....|.+.||++|..+++.| +|. +.-.++|- -.. +++..||..|.++
T Consensus 6 ~Qryl~~Il~~~~~~~~~vr~~Al~~l~~il~qGLvnP~-----~cvp~lIA----L~t--------s~~~~ir~~A~~~ 68 (187)
T PF12830_consen 6 VQRYLKNILELCLSSDDSVRLAALQVLELILRQGLVNPK-----QCVPTLIA----LET--------SPNPSIRSRAYQL 68 (187)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhcCCCChH-----HHHhHhhh----hhC--------CCChHHHHHHHHH
Confidence 4455667777777888999999999999999999 321 11122232 222 2466799999999
Q ss_pred HHHhhcCC
Q 005358 126 ISAIFSEE 133 (700)
Q Consensus 126 l~aLf~d~ 133 (700)
+..|+..-
T Consensus 69 l~~l~eK~ 76 (187)
T PF12830_consen 69 LKELHEKH 76 (187)
T ss_pred HHHHHHHh
Confidence 99999843
No 97
>PF14676 FANCI_S2: FANCI solenoid 2; PDB: 3S51_A 3S4Z_A 3S4W_A.
Probab=29.85 E-value=1.5e+02 Score=29.58 Aligned_cols=66 Identities=23% Similarity=0.247 Sum_probs=43.9
Q ss_pred HHHHHHHhccchhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHHHHHHhHHHHHHhhcccC
Q 005358 35 EICELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREMQRHSAVVRQLFHYKG 104 (700)
Q Consensus 35 EIA~~t~~s~~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrrns~~IK~l~~F~G 104 (700)
+|-..+++-+.....+|++.|.+|+-.++...-..=.++|.+||.+ +-..+.++..-|+++..|-.
T Consensus 40 ~IL~~~fk~h~~~r~~Ile~l~~rI~~~s~~~~~~~idlL~~lv~~----~p~~vle~~~~l~~~ld~l~ 105 (158)
T PF14676_consen 40 QILLELFKVHEMIRSEILEQLLNRIVTKSSSPSSQYIDLLSELVRK----APLTVLECSSKLKELLDYLS 105 (158)
T ss_dssp HHHHHHHHH-GGGHHHHHHHHHHHHHH--SS--HHHHHHHHHHHHH-----HHHHS-S-HHHHGGGGGTT
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHhcCccchhHHHHHHHHHHHH----ChHHHHHHHHHHHHHHHHHH
Confidence 4445555556667789999999999988766324558999999984 44567778888888876653
No 98
>KOG2259 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.72 E-value=1.2e+02 Score=36.90 Aligned_cols=78 Identities=17% Similarity=0.197 Sum_probs=55.2
Q ss_pred HHHHHhccchhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHHHHHHhHHHHHHhhcccCCCCCCCCchhhH
Q 005358 37 CELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREMQRHSAVVRQLFHYKGQLDPLKGDALNK 116 (700)
Q Consensus 37 A~~t~~s~~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrrns~~IK~l~~F~GppDpl~Gd~l~q 116 (700)
+.+.-+++ .|...-+|||..-+++.--.|++||+.-|+++..|+ ..-.....+|-.+. ++-..
T Consensus 398 ~~La~ssP-~FA~~aldfLvDMfNDE~~~VRL~ai~aL~~Is~~l-----~i~eeql~~il~~L-----------~D~s~ 460 (823)
T KOG2259|consen 398 CSLATSSP-GFAVRALDFLVDMFNDEIEVVRLKAIFALTMISVHL-----AIREEQLRQILESL-----------EDRSV 460 (823)
T ss_pred HHHHcCCC-CcHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHh-----eecHHHHHHHHHHH-----------HhcCH
Confidence 34444566 477789999999999999999999999999998873 11122334454444 12345
Q ss_pred HHHHHHHHHHHHhhc
Q 005358 117 AVRDMAHEAISAIFS 131 (700)
Q Consensus 117 ~VR~~AkEll~aLf~ 131 (700)
.||+++.|++.+.-=
T Consensus 461 dvRe~l~elL~~~~~ 475 (823)
T KOG2259|consen 461 DVREALRELLKNARV 475 (823)
T ss_pred HHHHHHHHHHHhcCC
Confidence 599999999887543
No 99
>PF12765 Cohesin_HEAT: HEAT repeat associated with sister chromatid cohesion
Probab=28.18 E-value=53 Score=25.63 Aligned_cols=26 Identities=35% Similarity=0.646 Sum_probs=22.8
Q ss_pred HHHHHHHHHhhccCCCchHHHHHHHH
Q 005358 49 KEVSDFILKRLEHKSPVVKQKALRLI 74 (700)
Q Consensus 49 ~eI~dyLlkRL~~ks~hVKlKaLKIL 74 (700)
.+|.+.|.+||.+.++.|+--||.+|
T Consensus 17 ~~v~~~i~~rl~D~s~~VR~aav~ll 42 (42)
T PF12765_consen 17 SDVQSAIIRRLSDSSPSVREAAVDLL 42 (42)
T ss_pred HHHHHHHHHHhcCCChHHHHHHHHHC
Confidence 38999999999999999988887664
No 100
>PF08620 RPAP1_C: RPAP1-like, C-terminal; InterPro: IPR013929 Inhibition of RNA polymerase II-associated protein 1 (RPAP1) synthesis in Saccharomyces cerevisiae (Baker's yeast) results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11 []. This entry represents the C-terminal region that contains the motif GLHHH. This region is conserved from yeast to humans.
Probab=27.63 E-value=85 Score=27.77 Aligned_cols=22 Identities=36% Similarity=0.440 Sum_probs=18.3
Q ss_pred CCCCCchhhHHHHHHHHHhccc
Q 005358 24 EDKVTPVYKLEEICELLRSSHV 45 (700)
Q Consensus 24 dd~PtPGYl~~EIA~~t~~s~~ 45 (700)
|+--.|||-+.|++.+++++..
T Consensus 32 ~~p~~aGYTi~El~~L~RSsv~ 53 (73)
T PF08620_consen 32 EDPEAAGYTIQELFHLSRSSVP 53 (73)
T ss_pred CCCCcCCcCHHHHHHHHhcCcH
Confidence 4555899999999999998754
No 101
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=24.55 E-value=1.4e+02 Score=29.55 Aligned_cols=57 Identities=16% Similarity=0.146 Sum_probs=46.0
Q ss_pred HHhhcCCcccCCCHHHHHHHHHHHh-hcCHHHHHHHHHHHhCCchHHHHHHHHHHHHH
Q 005358 275 TIVTYGGVRLQPTRDAIQVFLVEAA-KLDALAMSRALEAKLQSPLWQVRMKAICVLES 331 (700)
Q Consensus 275 ~i~T~gGvr~~PSreeLq~Fl~~c~-~Ld~e~V~elL~~kL~~~~WQvrlRALcvIEa 331 (700)
+++...|.|.+|.|..|-.++.... -++.+.|.+.|.++.....--+-+|.|-.++.
T Consensus 15 ~~L~~~GlR~T~qR~~IL~~l~~~~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e 72 (169)
T PRK11639 15 KLCAQRNVRLTPQRLEVLRLMSLQPGAISAYDLLDLLREAEPQAKPPTVYRALDFLLE 72 (169)
T ss_pred HHHHHcCCCCCHHHHHHHHHHHhcCCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHH
Confidence 4455569999999999999998765 49999999999988766666788888866644
No 102
>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=24.17 E-value=1.5e+02 Score=33.16 Aligned_cols=66 Identities=14% Similarity=0.116 Sum_probs=47.1
Q ss_pred cccCCCCCCCchhhHHHHHHHHHhccchhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHH
Q 005358 19 GATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRR 87 (700)
Q Consensus 19 kATSddd~PtPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r 87 (700)
+-..+++...=+.-+.=|+.+. .+ +.+..+...+.+-|.+++|+|+.||+-.|.++++..+..+..
T Consensus 86 kdl~~~n~~~~~lAL~~l~~i~--~~-~~~~~l~~~v~~ll~~~~~~VRk~A~~~l~~i~~~~p~~~~~ 151 (526)
T PF01602_consen 86 KDLNSPNPYIRGLALRTLSNIR--TP-EMAEPLIPDVIKLLSDPSPYVRKKAALALLKIYRKDPDLVED 151 (526)
T ss_dssp HHHCSSSHHHHHHHHHHHHHH---SH-HHHHHHHHHHHHHHHSSSHHHHHHHHHHHHHHHHHCHCCHHG
T ss_pred HhhcCCCHHHHHHHHhhhhhhc--cc-chhhHHHHHHHHHhcCCchHHHHHHHHHHHHHhccCHHHHHH
Confidence 3344444444455566666664 32 577889999999999999999999999999999876554443
No 103
>PF05598 DUF772: Transposase domain (DUF772); InterPro: IPR008490 This presumed domain is found at the N terminus of transposase insH and other related transposases.
Probab=23.56 E-value=1.9e+02 Score=24.38 Aligned_cols=64 Identities=22% Similarity=0.303 Sum_probs=41.8
Q ss_pred CchHHHHHHHHHHHHhc-CChhhHHHHHHhHHHHHHhhcc---cCCCCCCCCchhhHHHH-HHHHHHHHHhhcC
Q 005358 64 PVVKQKALRLIKYSVGK-SGTDFRREMQRHSAVVRQLFHY---KGQLDPLKGDALNKAVR-DMAHEAISAIFSE 132 (700)
Q Consensus 64 ~hVKlKaLKILkyLc~~-Gs~~F~r~lrrns~~IK~l~~F---~GppDpl~Gd~l~q~VR-~~AkEll~aLf~d 132 (700)
|.+.+|+| |++|+..- ...+....++.+..+..-|. + ...||. .+++.-.+ -...++++.||++
T Consensus 7 ~~~ml~~l-l~~~~~~~~S~r~l~~~l~~~~~~r~~~g-~~~~~~~pd~---stl~rfr~rl~~~~~~~~lf~~ 75 (77)
T PF05598_consen 7 PRMMLKAL-LLKYLFGLRSDRELEERLRDNLSFRYFCG-LSLEEPVPDH---STLSRFRKRLIQHGLIEKLFDQ 75 (77)
T ss_pred HHHHHHHH-HHHHHHhcchHHHHHhhHhhhhHHHHHHh-cccCCCCCCh---HHHHHHHHHHhhccHHHHHHHH
Confidence 45556655 77888876 66777778888887777666 4 334443 67775443 3444689998863
No 104
>PF14225 MOR2-PAG1_C: Cell morphogenesis C-terminal
Probab=23.26 E-value=1.3e+02 Score=32.32 Aligned_cols=68 Identities=18% Similarity=0.309 Sum_probs=41.5
Q ss_pred hHHHHHHHHHhcc-chhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHHHHHHhHHHHHHhhccc
Q 005358 32 KLEEICELLRSSH-VSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREMQRHSAVVRQLFHYK 103 (700)
Q Consensus 32 l~~EIA~~t~~s~-~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrrns~~IK~l~~F~ 103 (700)
.+..+++..++.. -+.-.+++.+|+.=|.++-+-+|.|+|+||++|+.+-.-+ +- ...++|+-+..+-
T Consensus 169 fl~~v~~~l~~~f~P~~~~~~l~~Ll~lL~n~~~w~~~~~L~iL~~ll~~~d~~--~~--~~~dlispllrlL 237 (262)
T PF14225_consen 169 FLSQVVSYLREAFFPDHEFQILTFLLGLLENGPPWLRRKTLQILKVLLPHVDMR--SP--HGADLISPLLRLL 237 (262)
T ss_pred HHHHHHHHHHHHhCchhHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHhccccCC--CC--cchHHHHHHHHHh
Confidence 3445555544421 1223467777888888887889999999999988765333 11 4445555554443
No 105
>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=23.25 E-value=3.2e+02 Score=29.32 Aligned_cols=45 Identities=22% Similarity=0.141 Sum_probs=28.9
Q ss_pred HHhhcCHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhH
Q 005358 297 EAAKLDALAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKF 341 (700)
Q Consensus 297 ~c~~Ld~e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~ 341 (700)
+....+.......|.+.|..+.|.++.+|+.++-.|+........
T Consensus 97 ~~~~~~~~~~~~~fl~ll~~~D~~i~~~a~~iLt~Ll~~~~~~~~ 141 (312)
T PF03224_consen 97 ELAKQDDSDPYSPFLKLLDRNDSFIQLKAAFILTSLLSQGPKRSE 141 (312)
T ss_dssp HHHH-TTH--HHHHHHH-S-SSHHHHHHHHHHHHHHHTSTTT--H
T ss_pred HhcccccchhHHHHHHHhcCCCHHHHHHHHHHHHHHHHcCCcccc
Confidence 333333333666666688889999999999999999998765444
No 106
>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=22.87 E-value=1.7e+02 Score=26.82 Aligned_cols=65 Identities=15% Similarity=0.242 Sum_probs=40.4
Q ss_pred hHHHHHHHHHhhccCC----CchHHHHHHHHHHHHhcCChhhHHHHHHhHHHHHHhhcccCCCCCCCCchhhHHHHHHHH
Q 005358 48 GKEVSDFILKRLEHKS----PVVKQKALRLIKYSVGKSGTDFRREMQRHSAVVRQLFHYKGQLDPLKGDALNKAVRDMAH 123 (700)
Q Consensus 48 ~~eI~dyLlkRL~~ks----~hVKlKaLKILkyLc~~Gs~~F~r~lrrns~~IK~l~~F~GppDpl~Gd~l~q~VR~~Ak 123 (700)
+..|++++.+-|+... ..+..++|+++++.+.....+.... ..++..+.++-.. +. .|.+|-
T Consensus 80 ~~~i~~~l~~~l~~~~~~~~~~~~~~~L~~l~s~i~~~~~~~i~~----~~~l~~~~~~l~~-~~---------~~~~A~ 145 (148)
T PF08389_consen 80 SPDILEILSQILSQSSSEANEELVKAALKCLKSWISWIPIELIIN----SNLLNLIFQLLQS-PE---------LREAAA 145 (148)
T ss_dssp HHHHHHHHHHHHHHHCHCCHHHHHHHHHHHHHHHTTTS-HHHHHS----SSHHHHHHHHTTS-CC---------CHHHHH
T ss_pred HHHHHHHHHHHHHhhccccHHHHHHHHHHHHHHHHHhCCHHHhcc----HHHHHHHHHHcCC-HH---------HHHHHH
Confidence 3567777777777544 6677999999999998555444433 2355555444432 22 267776
Q ss_pred HHH
Q 005358 124 EAI 126 (700)
Q Consensus 124 Ell 126 (700)
|++
T Consensus 146 ~cl 148 (148)
T PF08389_consen 146 ECL 148 (148)
T ss_dssp HHH
T ss_pred HhC
Confidence 664
No 107
>cd08330 CARD_ASC_NALP1 Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins. Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They se
Probab=22.52 E-value=1.5e+02 Score=26.32 Aligned_cols=51 Identities=10% Similarity=0.167 Sum_probs=33.2
Q ss_pred hHHHHHHHHHh--hccC-------CCchHHHHHHHHHHHHhcCC---hhhHHHHHH-hHHHHHH
Q 005358 48 GKEVSDFILKR--LEHK-------SPVVKQKALRLIKYSVGKSG---TDFRREMQR-HSAVVRQ 98 (700)
Q Consensus 48 ~~eI~dyLlkR--L~~k-------s~hVKlKaLKILkyLc~~Gs---~~F~r~lrr-ns~~IK~ 98 (700)
+..|+|+|+.+ |... .+.-+-|+-++|+.|..+|. ..|+..|+. +...++.
T Consensus 17 v~~ilD~L~~~~Vit~e~~~~I~a~~T~~~kar~Lld~l~~kG~~A~~~F~~~L~e~~p~L~~~ 80 (82)
T cd08330 17 VDPILDKLHGKKVITQEQYSEVRAEKTNQEKMRKLFSFVRSWGASCKDIFYQILREEEPYLVED 80 (82)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHcCCCcHHHHHHHHHHHHccCHHHHHHHHHHHHHhChHHHhH
Confidence 45666666664 2211 24668999999999999886 567777773 3344444
No 108
>PF14663 RasGEF_N_2: Rapamycin-insensitive companion of mTOR RasGEF_N domain
Probab=22.18 E-value=1.5e+02 Score=27.72 Aligned_cols=33 Identities=18% Similarity=0.243 Sum_probs=29.1
Q ss_pred HHHHHHHHHhhccCCCchHHHHHHHHHHHHhcC
Q 005358 49 KEVSDFILKRLEHKSPVVKQKALRLIKYSVGKS 81 (700)
Q Consensus 49 ~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~G 81 (700)
.=.+++|.+.|.+.++-|-.+|++||.-.|...
T Consensus 7 ~w~i~lLv~QL~D~~~~V~~~A~~iL~e~c~~~ 39 (115)
T PF14663_consen 7 DWGIELLVTQLYDPSPEVVAAALEILEEACEDK 39 (115)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhch
Confidence 457899999999999999999999999999866
No 109
>KOG2011 consensus Sister chromatid cohesion complex Cohesin, subunit STAG/IRR1/SCC3 [Cell cycle control, cell division, chromosome partitioning]
Probab=22.14 E-value=2.6e+02 Score=35.69 Aligned_cols=48 Identities=17% Similarity=0.140 Sum_probs=40.3
Q ss_pred HHHHHHHHHhccchhhH-HHHHHHHHhhccCCCchHHHHHHHHHHHHhc
Q 005358 33 LEEICELLRSSHVSIGK-EVSDFILKRLEHKSPVVKQKALRLIKYSVGK 80 (700)
Q Consensus 33 ~~EIA~~t~~s~~s~~~-eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~ 80 (700)
++||.-|....|+-|++ .-+.|+-==|.+|..-|+++|||+|.||..+
T Consensus 308 iqeLgiWi~~yP~~Fl~dsYLKYiGWtLsDk~~~VRl~~lkaL~~L~e~ 356 (1048)
T KOG2011|consen 308 IQELGIWIKSYPEIFLSDSYLKYIGWTLSDKNGTVRLRCLKALIKLYEK 356 (1048)
T ss_pred HHHHHHHHHhccHHHhcchHHHHhcceeecCccHHHHHHHHHHHHHHhc
Confidence 67788888777755544 5778888889999999999999999999987
No 110
>KOG1078 consensus Vesicle coat complex COPI, gamma subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.01 E-value=3.3e+02 Score=33.86 Aligned_cols=106 Identities=18% Similarity=0.128 Sum_probs=73.4
Q ss_pred HHHHHHHhhcCCcccCCCHHHHHHHHHHHhhcCHH---HHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHHHH
Q 005358 270 EKLLETIVTYGGVRLQPTRDAIQVFLVEAAKLDAL---AMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSIILS 346 (700)
Q Consensus 270 ~~LVe~i~T~gGvr~~PSreeLq~Fl~~c~~Ld~e---~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~ 346 (700)
.+||.. .+.+++|..-.+-.+.+-..+|..-+.. .+...|+.+|.++..-|.++|--+|-+|-..-..
T Consensus 208 sklv~~-~~~~~~~~~~A~~~lir~~~~~l~~~~~~~s~~~~fl~s~l~~K~emV~~EaArai~~l~~~~~r-------- 278 (865)
T KOG1078|consen 208 SKLVQK-FTRGSLKSPLAVCMLIRIASELLKENQQADSPLFPFLESCLRHKSEMVIYEAARAIVSLPNTNSR-------- 278 (865)
T ss_pred HHHHHH-HccccccchhHHHHHHHHHHHHhhhcccchhhHHHHHHHHHhchhHHHHHHHHHHHhhccccCHh--------
Confidence 445554 3446777777777777777777765544 6677788888888888888877666655443221
Q ss_pred HHHhhhHHHhhhhcCCChhHHHHHHHHHHHhcccccCC
Q 005358 347 YFCENNDVVVKCSESPQSSLREKANKVLSLLGEEQAGG 384 (700)
Q Consensus 347 Yf~eN~~~L~r~~~s~q~~LReKA~KVL~lLg~~~~~~ 384 (700)
-+.---..|+.+..++...||-+|.|+|..+-.--+..
T Consensus 279 ~l~pavs~Lq~flssp~~~lRfaAvRtLnkvAm~~P~~ 316 (865)
T KOG1078|consen 279 ELAPAVSVLQLFLSSPKVALRFAAVRTLNKVAMKHPQA 316 (865)
T ss_pred hcchHHHHHHHHhcCcHHHHHHHHHHHHHHHHHhCCcc
Confidence 11223367888999999999999999999986654443
No 111
>KOG1242 consensus Protein containing adaptin N-terminal region [Translation, ribosomal structure and biogenesis]
Probab=21.92 E-value=3.5e+02 Score=32.40 Aligned_cols=113 Identities=15% Similarity=0.155 Sum_probs=68.9
Q ss_pred hHHHHHHHHhhcCCcccCCCHHHHHHHHHHHhh-cCHH---HHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHH
Q 005358 268 REEKLLETIVTYGGVRLQPTRDAIQVFLVEAAK-LDAL---AMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSI 343 (700)
Q Consensus 268 ~E~~LVe~i~T~gGvr~~PSreeLq~Fl~~c~~-Ld~e---~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~ 343 (700)
|+..++-.+++.-|-+..==|+.-..=++.... ++.. .++.=|..-|.+..||.++-+|-+|-.+...... .
T Consensus 213 yiv~~lp~il~~~~d~~~~Vr~Aa~~a~kai~~~~~~~aVK~llpsll~~l~~~kWrtK~aslellg~m~~~ap~----q 288 (569)
T KOG1242|consen 213 YIVPILPSILTNFGDKINKVREAAVEAAKAIMRCLSAYAVKLLLPSLLGSLLEAKWRTKMASLELLGAMADCAPK----Q 288 (569)
T ss_pred hHHhhHHHHHHHhhccchhhhHHHHHHHHHHHHhcCcchhhHhhhhhHHHHHHHhhhhHHHHHHHHHHHHHhchH----H
Confidence 678888888887766543223222222222211 3332 3333333334445999999999999877654431 2
Q ss_pred HHHHHHhhhHHHhhhhcCCChhHHHHHHHHHHHhcccccCC
Q 005358 344 ILSYFCENNDVVVKCSESPQSSLREKANKVLSLLGEEQAGG 384 (700)
Q Consensus 344 v~~Yf~eN~~~L~r~~~s~q~~LReKA~KVL~lLg~~~~~~ 384 (700)
+..++..-...|..-....+..||+.+.+.|..++.-..+.
T Consensus 289 Ls~~lp~iiP~lsevl~DT~~evr~a~~~~l~~~~svidN~ 329 (569)
T KOG1242|consen 289 LSLCLPDLIPVLSEVLWDTKPEVRKAGIETLLKFGSVIDNP 329 (569)
T ss_pred HHHHHhHhhHHHHHHHccCCHHHHHHHHHHHHHHHHhhccH
Confidence 33444444466666677778999999999998888655444
No 112
>PF07814 WAPL: Wings apart-like protein regulation of heterochromatin; InterPro: IPR022771 This entry contains sequences expressed in eukaryotic organisms (metazoa, fungi, plants) bearing high similarity to the WAPL conserved region of D. melanogaster wings apart-like protein. This protein is involved in the regulation of heterochromatin structure []. hWAPL (Q7Z5K2 from SWISSPROT), the human homologue, is found to play a role in the development of cervical carcinogenesis, and is thought to have similar functions to Drosophila wapl protein []. Malfunction of the hWAPL pathway is thought to activate an apoptotic pathway that consequently leads to cell death []. This entry includes proteins from metazoa, fungi and plants.
Probab=21.87 E-value=2.2e+02 Score=31.63 Aligned_cols=59 Identities=20% Similarity=0.297 Sum_probs=44.5
Q ss_pred hHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCChhhHHHHHHhHHHHHHhhcccCCCC
Q 005358 48 GKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREMQRHSAVVRQLFHYKGQLD 107 (700)
Q Consensus 48 ~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs~~F~r~lrrns~~IK~l~~F~GppD 107 (700)
+.+-++||+.+|. ++.-...|++-+|.-+-.-..+.|++.+|.|-.+=|-+....+.+|
T Consensus 19 f~Dev~ylld~l~-~~~~~s~Rr~sll~La~K~~~~~Fr~~~ra~g~~~~l~~~l~~~~~ 77 (361)
T PF07814_consen 19 FADEVEYLLDGLE-SSSSSSVRRSSLLELASKCADPQFRRQFRAHGLVKRLFKALSDAPD 77 (361)
T ss_pred HHHHHHHHHhhcc-cCCCccHHHHHHHHHHHHhCCHHHHHHHHHcCcHHHHHHHhccccc
Confidence 3688899999999 4433457888888887778899999999999775555555555444
No 113
>KOG1967 consensus DNA repair/transcription protein Mms19 [Replication, recombination and repair; Transcription]
Probab=21.54 E-value=2.8e+02 Score=35.07 Aligned_cols=78 Identities=14% Similarity=0.146 Sum_probs=53.6
Q ss_pred ccCCCCCC-CchhhHHHHHHHHHhccchhhHHHHHHHHHhhccCCCchHHHHHHHHHHHHhcCC-hhhHHHHHHhHHHHH
Q 005358 20 ATSDEDKV-TPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSG-TDFRREMQRHSAVVR 97 (700)
Q Consensus 20 ATSddd~P-tPGYl~~EIA~~t~~s~~s~~~eI~dyLlkRL~~ks~hVKlKaLKILkyLc~~Gs-~~F~r~lrrns~~IK 97 (700)
++-||+.. .--|+-.-+....-+.+ .|.......|+.||+.+.|.+|.-+|++|+-||.+=. .+.....+..-..||
T Consensus 225 ppk~D~~~I~reDL~~sLr~al~stP-~Fa~~~lp~LlEKL~as~~~~K~DsL~~L~ec~~~ygv~~~~~~~~~lWsaik 303 (1030)
T KOG1967|consen 225 PPKDDTITIRREDLKASLRSALVSTP-SFAPFALPLLLEKLNASDPSAKVDSLDTLNECCLKYGVRRMLPAQKKLWSAIK 303 (1030)
T ss_pred CCCCCcccccHHHHHHHHHHHHhcCc-cchhhHHHHHHHHhccccchhhhhHHHHHHHHHHHhCchhhhhhHHHHHHHHH
Confidence 34444444 22444444555555665 5778899999999999999999999999999997543 444444455555565
Q ss_pred H
Q 005358 98 Q 98 (700)
Q Consensus 98 ~ 98 (700)
.
T Consensus 304 ~ 304 (1030)
T KOG1967|consen 304 P 304 (1030)
T ss_pred H
Confidence 4
No 114
>PF03700 Sorting_nexin: Sorting nexin, N-terminal domain ; InterPro: IPR005329 SNXs are hydrophilic molecules that are localized in the cytoplasm and have the potential for membrane association either through their lipid-binding PX domains (IPR001683 from INTERPRO) or through protein-protein interactions with membrane-associated protein complexes []. Indeed, several of the SNXs require several targeting motifs for their appropriate cellular localization. In almost every case studied, mammalian SNXs can be shown to have a role in protein sorting, with the most commonly used experimental model being plasma-membrane receptor endocytosis and sorting through the endosomal pathway. However, it is equally probable that SNXs sort vesicles that are not derived from the plasma membrane, and have a function in the accurate targeting of these vesicles and their cargo. The N-terminal domain appears to be specific to sorting nexins 1 and 2. SNX1 is both membrane-associated and cytosolic, where it probably exists as a tetramer in large protein complexes and may hetero-oligomerize with SNX2.; GO: 0008565 protein transporter activity, 0006886 intracellular protein transport
Probab=21.38 E-value=1.4e+02 Score=29.12 Aligned_cols=60 Identities=23% Similarity=0.353 Sum_probs=33.3
Q ss_pred cccccccccccccccCCCccccccccccCCCCCccccccCCCCC---CCccccc--cCCchhhhccc----cccCCCCC
Q 005358 475 GKEHVEDLFSGMTVDSKPVASGNLLAADKSGSEPFDDIFGSHTE---ILPKQEN--QKNNFNDLMAG----FSINEDQL 544 (700)
Q Consensus 475 ~~~~~~dlfsg~tv~~~~~~~~~~~~~~~~~~~~~~d~fg~~~~---~~~~~~~--~~~~~~~l~~~----~~~~~~~~ 544 (700)
....++|||.|--+..+ .+..+ ++.. |||..... --+.++| +..+-.||.|. ||++....
T Consensus 22 d~deGEDiFt~~~s~~~-------~~~~~--~epa-~lp~e~~S~~~ng~~~~ng~~sDD~~DLFAEATvElSLDsp~n 90 (129)
T PF03700_consen 22 DDDEGEDIFTSAVSTLE-------SPPSK--PEPA-SLPSEEISTKSNGPKEENGVHSDDDQDLFAEATVELSLDSPEN 90 (129)
T ss_pred ccccccccccccccccc-------CCCCC--CCcc-cccccccccccCCCCccccccccchhhhhhhccccccccCCcc
Confidence 67789999998543211 11122 2333 77754433 1333333 45567889886 67776643
No 115
>PF08252 Leader_CPA1: arg-2/CPA1 leader peptide ; InterPro: IPR013203 In this family there are leaders peptides involved in the regulation of the glutaminase subunit (small subunit) of arginine-specific carbamoyl phosphate synthetase. In Neurospora crassa it is a small upstream ORF of 24 codons above the arg-2 locus []. In yeast it is the leader peptide of the CPA1 gene. The 5' region of CPA1 mRNA contains a 25 codon upstream open reading frame. The leader peptide, the product of the upstream open reading frame, plays an essential, negative role in the specific repression of CPA1 by arginine [].; PDB: 2XL1_A.
Probab=21.30 E-value=21 Score=25.23 Aligned_cols=7 Identities=43% Similarity=0.748 Sum_probs=5.7
Q ss_pred ccccccc
Q 005358 690 DFISVSL 696 (700)
Q Consensus 690 ~~~~~~~ 696 (700)
||||||+
T Consensus 12 DYiSDhi 18 (24)
T PF08252_consen 12 DYISDHI 18 (24)
T ss_dssp HHHHHHH
T ss_pred HHHHHHH
Confidence 8888886
No 116
>PF12031 DUF3518: Domain of unknown function (DUF3518); InterPro: IPR021906 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 260 amino acids in length. This domain is found associated with PF01388 from PFAM.
Probab=21.21 E-value=4.6e+02 Score=28.46 Aligned_cols=96 Identities=15% Similarity=0.200 Sum_probs=72.7
Q ss_pred HHHHHHHHhhhhcccCCCCCCCc---------hhhHHHHHHHHHhc-cc---------hhhHHHHHHHHHhhc-cCCCch
Q 005358 7 AVESYWRSRMIDGATSDEDKVTP---------VYKLEEICELLRSS-HV---------SIGKEVSDFILKRLE-HKSPVV 66 (700)
Q Consensus 7 ~v~~~~~~~lV~kATSddd~PtP---------GYl~~EIA~~t~~s-~~---------s~~~eI~dyLlkRL~-~ks~hV 66 (700)
-++-.-||..=.-|...|+-|+- -|.+|=+++++-.. .+ +-++.+.+.|.+-|. ++.++.
T Consensus 110 ildGLLHWaVcpsa~A~Dpfp~~~~~~~lSPqrlaLEaLcKLsV~e~NVDliLaTpp~sRlE~l~~~L~r~l~~~e~~v~ 189 (257)
T PF12031_consen 110 ILDGLLHWAVCPSAEAQDPFPTAGPHSPLSPQRLALEALCKLSVIENNVDLILATPPFSRLERLFHTLVRLLGMREDQVC 189 (257)
T ss_pred HHHHHHHHHhccchhccCCCCCCCCCCCCCHHHHHHHHHHHhheeccCcceeeeCCCHHHHHHHHHHHHHHhccccchhH
Confidence 35677888888888888988862 28899999997521 11 124567888888888 555888
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHhHHHHHHhhccc
Q 005358 67 KQKALRLIKYSVGKSGTDFRREMQRHSAVVRQLFHYK 103 (700)
Q Consensus 67 KlKaLKILkyLc~~Gs~~F~r~lrrns~~IK~l~~F~ 103 (700)
+==|+-||-|||. |++.+-|.+......|-.|..|-
T Consensus 190 REfAvvlL~~La~-~~~~~~r~iA~q~~~i~~Li~Fi 225 (257)
T PF12031_consen 190 REFAVVLLSNLAQ-GDEAAARAIAMQKPCISHLIAFI 225 (257)
T ss_pred HHHHHHHHHHHhc-ccHHHHHHHHHhhchHHHHHHHH
Confidence 8889999999998 77788877777777788888776
No 117
>PF06878 Pkip-1: Pkip-1 protein; InterPro: IPR009672 This family consists of several Pkip-1 proteins, which seem to be specific to Nucleopolyhedroviruses. The function of this family is unknown although it has been found that Pkip-1 is not essential for virus replication in cell culture or by in vivo intrahaemocoelic injection [].
Probab=20.16 E-value=1.9e+02 Score=29.37 Aligned_cols=36 Identities=28% Similarity=0.148 Sum_probs=23.3
Q ss_pred ccchhhHHHHHHHHHhhc-cCC-Cc------hHHHHHHHHHHHHh
Q 005358 43 SHVSIGKEVSDFILKRLE-HKS-PV------VKQKALRLIKYSVG 79 (700)
Q Consensus 43 s~~s~~~eI~dyLlkRL~-~ks-~h------VKlKaLKILkyLc~ 79 (700)
....|+.=+..|+.+|-. ++. .+ |++||. +|||||.
T Consensus 115 n~~~F~kvl~qFv~Krn~~rk~~~~~lL~ELV~LKs~-lIKHLC~ 158 (163)
T PF06878_consen 115 NSKKFIKVLEQFVDKRNAYRKNNNNALLDELVLLKSN-LIKHLCI 158 (163)
T ss_pred hhHHHHHHHHHHHHHHHHHHcCchhhHHHHHHHHHHH-HHHHHHH
Confidence 334566667778887765 333 33 888875 7888884
No 118
>KOG2023 consensus Nuclear transport receptor Karyopherin-beta2/Transportin (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=20.02 E-value=1.2e+02 Score=37.03 Aligned_cols=61 Identities=16% Similarity=0.169 Sum_probs=47.2
Q ss_pred HHHHHHHHHHhCCchHHHHHHHHHHHHHHHhccCchhHHHHHHHHHhhhHHHhhhhcCCChhHHH
Q 005358 304 LAMSRALEAKLQSPLWQVRMKAICVLESILRKKDDEKFSIILSYFCENNDVVVKCSESPQSSLRE 368 (700)
Q Consensus 304 e~V~elL~~kL~~~~WQvrlRALcvIEaLl~s~~~d~~~~v~~Yf~eN~~~L~r~~~s~q~~LRe 368 (700)
+.+..+|.++|.+..|.+|=-++.++=|+..-.- +.+..|.-|-...+..|-....+.||.
T Consensus 392 ~~l~PlLk~~L~~~~W~vrEagvLAlGAIAEGcM----~g~~p~LpeLip~l~~~L~DKkplVRs 452 (885)
T KOG2023|consen 392 PILLPLLKEHLSSEEWKVREAGVLALGAIAEGCM----QGFVPHLPELIPFLLSLLDDKKPLVRS 452 (885)
T ss_pred HHHHHHHHHHcCcchhhhhhhhHHHHHHHHHHHh----hhcccchHHHHHHHHHHhccCccceee
Confidence 6789999999999999999999999988876321 234556666667777888887777775
Done!