Query 011515
Match_columns 484
No_of_seqs 194 out of 724
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 02:13:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011515.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011515hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1087 Cytosolic sorting prot 100.0 1.4E-70 3.1E-75 579.0 37.6 372 1-404 1-386 (470)
2 KOG1086 Cytosolic sorting prot 100.0 6.4E-52 1.4E-56 423.7 26.8 288 2-295 9-324 (594)
3 cd03568 VHS_STAM VHS domain fa 100.0 7.3E-42 1.6E-46 312.6 18.0 137 2-139 1-137 (144)
4 cd03569 VHS_Hrs_Vps27p VHS dom 100.0 7.2E-42 1.6E-46 311.9 17.2 137 2-139 5-141 (142)
5 cd03565 VHS_Tom1 VHS domain fa 100.0 2.1E-41 4.5E-46 308.6 16.5 136 2-138 2-141 (141)
6 cd03567 VHS_GGA VHS domain fam 100.0 7.6E-41 1.7E-45 304.2 16.2 131 2-136 2-137 (139)
7 smart00288 VHS Domain present 100.0 1.8E-38 3.8E-43 286.4 16.3 132 2-134 1-133 (133)
8 PF00790 VHS: VHS domain; Int 100.0 4.5E-37 9.7E-42 279.0 16.3 132 2-134 6-140 (140)
9 cd03561 VHS VHS domain family; 100.0 6.2E-37 1.4E-41 275.9 15.9 131 2-132 1-133 (133)
10 KOG2199 Signal transducing ada 100.0 1.8E-34 3.9E-39 293.6 24.4 265 2-270 9-368 (462)
11 cd00197 VHS_ENTH_ANTH VHS, ENT 99.9 2.3E-25 5E-30 195.1 13.0 109 2-110 1-114 (115)
12 KOG1818 Membrane trafficking a 99.9 4.8E-23 1E-27 222.6 9.9 144 3-148 10-154 (634)
13 PF03127 GAT: GAT domain; Int 99.8 7.9E-21 1.7E-25 163.6 8.4 94 179-272 3-96 (100)
14 cd03572 ENTH_epsin_related ENT 98.1 3.1E-05 6.7E-10 69.6 10.9 106 1-108 1-116 (122)
15 PF01417 ENTH: ENTH domain; I 98.1 3E-05 6.5E-10 69.2 10.5 105 2-109 4-119 (125)
16 cd03562 CID CID (CTD-Interacti 97.8 4.9E-05 1.1E-09 66.4 7.3 94 18-113 17-110 (114)
17 cd03571 ENTH_epsin ENTH domain 97.6 0.00064 1.4E-08 61.2 11.2 106 2-110 2-117 (123)
18 smart00273 ENTH Epsin N-termin 97.6 0.00091 2E-08 59.7 11.9 108 2-109 3-117 (127)
19 cd03564 ANTH_AP180_CALM ANTH d 97.3 0.0013 2.7E-08 58.2 9.1 78 2-79 1-78 (117)
20 KOG2056 Equilibrative nucleosi 96.8 0.01 2.2E-07 61.7 10.6 109 3-112 23-139 (336)
21 KOG2374 Uncharacterized conser 96.7 0.015 3.2E-07 62.8 11.6 135 2-140 8-152 (661)
22 smart00582 RPR domain present 96.0 0.022 4.8E-07 50.0 6.9 91 20-111 14-107 (121)
23 KOG0251 Clathrin assembly prot 94.3 0.11 2.4E-06 56.9 7.3 80 2-81 24-104 (491)
24 PF07651 ANTH: ANTH domain; I 92.2 0.48 1E-05 47.4 7.7 76 2-78 4-80 (280)
25 PF13646 HEAT_2: HEAT repeats; 90.9 3.4 7.3E-05 33.2 10.1 86 3-106 2-87 (88)
26 KOG2057 Predicted equilibrativ 90.4 1.4 3.1E-05 45.9 8.9 102 5-108 27-140 (499)
27 PF12348 CLASP_N: CLASP N term 89.3 3.9 8.4E-05 39.2 10.8 79 36-115 129-210 (228)
28 KOG2160 Armadillo/beta-catenin 88.5 1.5 3.2E-05 46.1 7.5 92 21-114 106-199 (342)
29 PF12717 Cnd1: non-SMC mitotic 83.0 12 0.00026 35.1 10.2 88 20-113 7-94 (178)
30 PF04818 CTD_bind: RNA polymer 81.7 3.5 7.5E-05 32.4 5.1 54 57-111 3-59 (64)
31 smart00229 RasGEFN Guanine nuc 79.5 33 0.00072 30.0 11.2 104 2-107 10-124 (127)
32 cd00020 ARM Armadillo/beta-cat 78.9 17 0.00036 30.1 8.8 69 38-108 49-117 (120)
33 PF12348 CLASP_N: CLASP N term 77.4 14 0.0003 35.5 8.8 96 15-113 17-125 (228)
34 PF12210 Hrs_helical: Hepatocy 74.8 7 0.00015 34.0 5.2 55 189-243 4-58 (96)
35 PF13646 HEAT_2: HEAT repeats; 74.4 17 0.00036 29.1 7.3 57 40-109 1-58 (88)
36 PF08167 RIX1: rRNA processing 71.1 38 0.00082 31.7 9.8 75 36-111 19-97 (165)
37 cd06224 REM Guanine nucleotide 69.4 71 0.0015 27.3 10.5 85 2-91 2-100 (122)
38 PF11841 DUF3361: Domain of un 65.1 24 0.00053 33.4 7.1 60 50-111 72-131 (160)
39 KOG2071 mRNA cleavage and poly 64.4 10 0.00022 42.5 5.1 78 31-110 33-110 (579)
40 PF06812 ImpA-rel_N: ImpA-rela 62.9 32 0.00068 27.0 6.4 58 18-75 1-59 (62)
41 KOG1077 Vesicle coat complex A 62.0 27 0.00059 40.3 7.8 72 23-102 96-168 (938)
42 cd00020 ARM Armadillo/beta-cat 60.3 33 0.00072 28.3 6.6 72 39-112 8-79 (120)
43 COG1059 Thermostable 8-oxoguan 59.9 34 0.00073 33.6 7.1 101 16-135 36-143 (210)
44 PRK09687 putative lyase; Provi 55.3 1.1E+02 0.0024 31.1 10.5 72 36-107 190-278 (280)
45 cd08779 Death_PIDD Death Domai 52.6 35 0.00076 28.7 5.3 42 90-134 33-74 (86)
46 KOG1293 Proteins containing ar 51.9 51 0.0011 37.6 7.9 74 38-112 461-534 (678)
47 PF01602 Adaptin_N: Adaptin N 51.1 1.1E+02 0.0023 32.9 10.2 76 27-111 68-143 (526)
48 smart00509 TFS2N Domain in the 50.7 81 0.0018 25.8 7.1 24 90-113 50-73 (75)
49 PF01602 Adaptin_N: Adaptin N 49.7 43 0.00092 36.0 6.8 88 19-110 132-220 (526)
50 cd00183 TFIIS_I N-terminal dom 48.4 49 0.0011 27.1 5.4 25 89-113 51-75 (76)
51 KOG1105 Transcription elongati 48.3 74 0.0016 33.1 7.9 75 36-115 6-80 (296)
52 PF06160 EzrA: Septation ring 48.0 4E+02 0.0088 29.9 14.3 79 57-140 161-248 (560)
53 cd08306 Death_FADD Fas-associa 47.5 52 0.0011 27.6 5.6 71 61-135 4-74 (86)
54 PF02854 MIF4G: MIF4G domain; 47.0 1E+02 0.0022 28.3 8.0 87 21-107 106-204 (209)
55 PF03670 UPF0184: Uncharacteri 46.8 53 0.0011 28.0 5.4 54 186-241 25-78 (83)
56 PF06798 PrkA: PrkA serine pro 46.5 16 0.00034 37.0 2.7 77 35-113 38-117 (254)
57 cd08319 Death_RAIDD Death doma 45.6 52 0.0011 27.7 5.3 70 62-135 5-74 (83)
58 PF11707 Npa1: Ribosome 60S bi 44.9 1.3E+02 0.0029 31.2 9.3 52 40-91 58-111 (330)
59 PF00618 RasGEF_N: RasGEF N-te 43.6 85 0.0018 26.4 6.4 57 72-131 32-102 (104)
60 smart00543 MIF4G Middle domain 43.5 95 0.0021 28.5 7.3 70 20-90 98-170 (200)
61 PF12783 Sec7_N: Guanine nucle 42.8 1.1E+02 0.0024 28.2 7.6 63 51-114 35-105 (168)
62 COG4477 EzrA Negative regulato 41.5 5.1E+02 0.011 29.3 13.3 41 97-140 211-251 (570)
63 PF05004 IFRD: Interferon-rela 40.9 1.9E+02 0.004 30.0 9.6 67 38-106 86-155 (309)
64 KOG1820 Microtubule-associated 39.9 1.9E+02 0.0041 34.2 10.4 91 20-115 354-447 (815)
65 PF11698 V-ATPase_H_C: V-ATPas 39.8 1.1E+02 0.0023 27.7 6.7 75 34-110 39-114 (119)
66 PF10508 Proteasom_PSMB: Prote 39.4 2.3E+02 0.0049 31.3 10.5 92 18-111 117-231 (503)
67 PF00618 RasGEF_N: RasGEF N-te 39.3 76 0.0016 26.7 5.5 73 2-76 7-94 (104)
68 cd08777 Death_RIP1 Death Domai 36.8 75 0.0016 26.8 5.0 70 62-134 5-75 (86)
69 PRK01005 V-type ATP synthase s 35.7 87 0.0019 30.8 5.9 61 52-112 63-125 (207)
70 smart00005 DEATH DEATH domain, 35.5 73 0.0016 25.9 4.7 69 62-134 8-77 (88)
71 KOG2075 Topoisomerase TOP1-int 35.2 1.4E+02 0.003 33.2 7.8 96 17-113 185-296 (521)
72 PF10508 Proteasom_PSMB: Prote 35.1 2.3E+02 0.0049 31.3 9.7 92 18-111 51-148 (503)
73 KOG1077 Vesicle coat complex A 34.5 1E+02 0.0023 35.8 6.9 73 35-111 326-398 (938)
74 PF02985 HEAT: HEAT repeat; I 34.3 1E+02 0.0022 20.5 4.4 30 40-69 2-31 (31)
75 PF12333 Ipi1_N: Rix1 complex 33.9 3.1E+02 0.0067 23.6 9.0 52 39-91 12-63 (102)
76 PF00531 Death: Death domain; 33.8 1.1E+02 0.0023 24.4 5.3 66 64-134 6-71 (83)
77 cd08317 Death_ank Death domain 33.6 97 0.0021 25.6 5.1 68 63-134 8-75 (84)
78 KOG1062 Vesicle coat complex A 33.6 1.9E+02 0.0042 34.1 8.8 103 21-132 162-277 (866)
79 PF07531 TAFH: NHR1 homology t 33.2 59 0.0013 28.4 3.8 33 80-112 7-39 (96)
80 KOG2236 Uncharacterized conser 32.4 64 0.0014 35.5 4.7 62 371-445 419-482 (483)
81 PTZ00429 beta-adaptin; Provisi 32.0 2.6E+02 0.0057 32.8 9.8 86 17-106 232-321 (746)
82 cd08805 Death_ank1 Death domai 31.8 1.2E+02 0.0026 25.7 5.3 69 62-134 7-75 (84)
83 PF14500 MMS19_N: Dos2-interac 31.3 2.4E+02 0.0052 28.6 8.4 77 36-114 78-156 (262)
84 PRK04778 septation ring format 31.2 8E+02 0.017 27.6 15.1 98 37-140 146-252 (569)
85 PF04740 LXG: LXG domain of WX 31.0 4E+02 0.0088 25.1 9.6 81 189-269 70-167 (204)
86 smart00549 TAFH TAF homology. 30.9 76 0.0017 27.5 4.0 33 80-112 6-38 (92)
87 PF14523 Syntaxin_2: Syntaxin- 30.4 2.9E+02 0.0064 23.0 7.7 80 188-268 4-92 (102)
88 PF12783 Sec7_N: Guanine nucle 29.9 2.7E+02 0.0058 25.6 7.9 71 39-111 74-146 (168)
89 PF11099 M11L: Apoptosis regul 29.1 1.6E+02 0.0034 28.3 6.2 65 24-88 48-115 (167)
90 KOG3192 Mitochondrial J-type c 29.1 1.2E+02 0.0025 29.0 5.2 44 216-259 55-111 (168)
91 PF13513 HEAT_EZ: HEAT-like re 29.0 85 0.0018 23.2 3.7 52 52-106 1-52 (55)
92 PF08328 ASL_C: Adenylosuccina 27.9 1.3E+02 0.0028 27.2 5.1 63 28-105 47-109 (115)
93 PLN03200 cellulose synthase-in 27.1 2.5E+02 0.0055 36.7 9.1 71 39-110 190-260 (2102)
94 cd01670 Death Death Domain: a 27.1 1.5E+02 0.0032 23.4 5.0 34 98-135 37-70 (79)
95 PF12755 Vac14_Fab1_bd: Vacuol 26.8 3.9E+02 0.0084 22.9 7.8 64 36-102 25-88 (97)
96 PF11864 DUF3384: Domain of un 26.0 4.4E+02 0.0096 28.7 9.9 93 19-111 8-117 (464)
97 PF09324 DUF1981: Domain of un 25.9 1.7E+02 0.0038 24.4 5.4 36 79-114 15-50 (86)
98 KOG3811 Transcription factor A 25.8 1.3E+02 0.0028 32.8 5.5 55 406-466 39-95 (434)
99 PF04961 FTCD_C: Formiminotran 25.1 1.8E+02 0.004 27.9 6.0 43 197-239 31-74 (184)
100 smart00229 RasGEFN Guanine nuc 25.0 3.2E+02 0.0068 23.7 7.2 44 73-116 36-89 (127)
101 TIGR01385 TFSII transcription 24.9 1.6E+02 0.0035 30.6 6.0 26 90-115 52-77 (299)
102 cd08318 Death_NMPP84 Death dom 24.7 1.9E+02 0.0041 24.2 5.4 69 62-135 10-78 (86)
103 PF14663 RasGEF_N_2: Rapamycin 24.2 1.8E+02 0.004 25.6 5.5 76 37-113 7-93 (115)
104 KOG4535 HEAT and armadillo rep 23.9 66 0.0014 35.9 3.0 45 25-69 131-181 (728)
105 cd06224 REM Guanine nucleotide 23.5 3.5E+02 0.0076 22.9 7.1 45 72-116 27-84 (122)
106 cd08804 Death_ank2 Death domai 23.1 1.8E+02 0.0038 24.4 4.9 67 62-132 7-73 (84)
107 PRK14148 heat shock protein Gr 22.9 3.6E+02 0.0079 26.4 7.6 66 188-262 41-109 (195)
108 PF12830 Nipped-B_C: Sister ch 22.5 3.7E+02 0.008 25.5 7.6 65 43-114 13-77 (187)
109 PRK14140 heat shock protein Gr 22.5 3.9E+02 0.0085 26.0 7.8 44 219-262 60-106 (191)
110 PRK09458 pspB phage shock prot 21.9 1.1E+02 0.0024 25.6 3.2 25 212-236 37-61 (75)
111 KOG1511 Mevalonate kinase MVK/ 21.7 1.9E+02 0.0042 31.0 5.8 44 217-260 259-308 (397)
112 KOG4508 Uncharacterized conser 21.7 2.6E+02 0.0056 30.5 6.7 95 35-134 386-510 (522)
113 PF09712 PHA_synth_III_E: Poly 21.4 1.6E+02 0.0034 30.5 5.1 91 36-130 189-281 (293)
114 PRK14162 heat shock protein Gr 21.1 4E+02 0.0087 26.0 7.5 45 218-262 61-108 (194)
115 PF10363 DUF2435: Protein of u 21.0 4.3E+02 0.0094 22.5 6.9 68 3-71 6-76 (92)
116 COG5369 Uncharacterized conser 21.0 2.6E+02 0.0056 31.9 6.8 89 22-111 452-545 (743)
117 PRK14154 heat shock protein Gr 20.8 3.6E+02 0.0077 26.7 7.1 44 219-262 75-121 (208)
118 PF11083 Streptin-Immun: Lanti 20.7 4.9E+02 0.011 22.9 7.1 31 239-269 51-81 (99)
119 PTZ00429 beta-adaptin; Provisi 20.7 6.5E+02 0.014 29.6 10.4 35 27-61 94-128 (746)
120 PF09758 FPL: Uncharacterised 20.1 2.6E+02 0.0057 26.2 5.8 48 70-117 15-62 (149)
121 cd08803 Death_ank3 Death domai 20.1 2.7E+02 0.0058 23.4 5.4 69 62-134 7-75 (84)
122 PF08711 Med26: TFIIS helical 20.1 1.9E+02 0.0041 21.6 4.1 20 94-113 33-52 (53)
No 1
>KOG1087 consensus Cytosolic sorting protein GGA2/TOM1 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.4e-70 Score=579.01 Aligned_cols=372 Identities=43% Similarity=0.708 Sum_probs=295.9
Q ss_pred ChHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcch
Q 011515 1 MVNSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEK 80 (484)
Q Consensus 1 ~v~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask 80 (484)
||+.+|+|||++.+.+|||++||+|||+||.+..+++||+|+|+|||++++++||++||+|||+||||||+.||.+|++|
T Consensus 1 ~v~~~IdkAT~~~l~~pDWa~NleIcD~IN~~~~~~~eAvralkKRi~~k~s~vq~lALtlLE~cvkNCG~~fh~~Va~k 80 (470)
T KOG1087|consen 1 SVGKLIDKATSESLAEPDWALNLEICDLINSTEGGPKEAVRALKKRLNSKNSKVQLLALTLLETCVKNCGYSFHLQVASK 80 (470)
T ss_pred ChHHHHHHhhcccccCccHHHHHHHHHHHhcCccCcHHHHHHHHHHhccCCcHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhccC-CChhHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCC-CCC--
Q 011515 81 NVLHEMVKIARKK-PDTHVKEKILILIDTWQEAFGGPRARYPQYYAAYQELLRAGAVFPQRSERSAPVFTPPQT-HPL-- 156 (484)
Q Consensus 81 ~FLneLvkLv~~k-~d~~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~kGi~FP~~~e~~~piftPp~~-~p~-- 156 (484)
+||++||++++++ ++..||+|||.||++|+++|++...+++.|+.+|++|+++||+||.+++.+-++++||.. ++.
T Consensus 81 ~fL~emVk~~k~~~~~~~Vr~kiL~LI~~W~~af~~~~~~~~~~~~~y~~l~~~G~~FP~r~~~sl~~~~pp~~~~~~~~ 160 (470)
T KOG1087|consen 81 EFLNEMVKRPKNKPRDLKVREKILELIDTWQQAFCGPDGYLPDYYQIYDELRRKGVEFPQRDEESLAVLTPPAVLRPAPE 160 (470)
T ss_pred HHHHHHHhccccCCcchhHHHHHHHHHHHHHHHccCCCCcchhHHHHHHHHHHcCCcCCCCccccccccCCCCCCCCCCC
Confidence 9999999999998 899999999999999999999966789999999999999999999998888777776532 111
Q ss_pred ---CCCCCCCCCchhh--h-HhHhhhcccCCCCCCHHHHHHHHHHHHHHHHHHhhcCCCCCccCchHHHHHHHHHHHHHH
Q 011515 157 ---TSYPQNFRNPEHQ--Q-EAAEASAESEFPTLSLTEIQNARGIMDVLAEMLNALDPNNKEGLRQEVIVDLVDQCRTYK 230 (484)
Q Consensus 157 ---Ss~P~~lr~a~~~--~-~~~e~~~~~e~~~~~lseLe~ak~nv~LL~EML~~~~P~~~e~~d~Eli~EL~~~Cr~~q 230 (484)
..+|.+ .++.. . .........++..+++++|++|+++|+||+|||.+++|++++..++|++++|+++||.+|
T Consensus 161 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~seLe~~~~~~~ll~emL~~v~p~~~e~~~~el~~~L~~qcr~~q 238 (470)
T KOG1087|consen 161 PQEQSGPPN--EANASMKSMAGYPTEATPEVSTLSLSELESVKGKADLLSEMLNAVDPSDEEAAKDELLVDLVEQCRSKQ 238 (470)
T ss_pred chhhcCCcc--ccccccccccccchhhhhhhhhhhHHHHHHHHHHHHHHHHHHhccCCCCcchhHHHHHHHHHHHHHHHH
Confidence 112222 11111 1 111222234567788899999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhccCCHHHHHHHhhhhHHHHHHHHHHHhhhcCCccccccCCCCCCCCCCCCccccCCCC----CCCCCCCCCC
Q 011515 231 QRVVHLVNSTADESLLCQGLQLNDDLQRLLAKHESFASGKSAQTAQTDKPKTESKSSEALVDVDGP----LVDTGDATKQ 306 (484)
Q Consensus 231 ~rV~rLI~~~~DEelL~eLL~aNDeL~~vL~rYe~l~~g~~~~~~~~~~~~~~~~~~~~LiD~~~~----~~~~~~~~~~ 306 (484)
+||++||+++.||++|+++|++||+|++||++||++.+|..... +.+. +.....+|.++. .....+...+
T Consensus 239 ~rv~~Li~~~~DE~ll~~lL~lND~L~~vL~~ye~~~~g~s~~~--~~~~----e~~~~p~~~~~~~~~~~~s~~~~~~~ 312 (470)
T KOG1087|consen 239 RRVMHLIEETSDEELLCELLKLNDELQRVLERYERIASGSSVAT--TSKS----ETASDPVDQSSSLLDKDDSSIDLNDS 312 (470)
T ss_pred HHHHHHHHHhccHHHHHHHHHHhHHHHHHHHHHHHHhccccccc--cccc----ccCCCccccCccccccCcCccccccc
Confidence 99999999999999999999999999999999999999932211 1111 222244444332 2334556677
Q ss_pred CCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCccccccCCCCCCCCCCCCccccccCCCCCCCCCCcccchhhH
Q 011515 307 PDGRTTSNGGAGAQPLNQLLLPAPAAANGSSPPAAVNPKIDLLSGDDYSSPKEDTSLALVPVGVPQPNTPVSSQQNALVL 386 (484)
Q Consensus 307 ~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~d~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 386 (484)
+.+|+++++ ..+.+.+..+.. .....+|.| +.+++++++++++++|+++.++++.+
T Consensus 313 ~~~~ss~~~-----------~~~~~~~~~~~~--~l~~d~~~l-----------~~~~~~~l~~~~p~~~~~~~~~~~~~ 368 (470)
T KOG1087|consen 313 LASRSSSTG-----------ISATPSSEQPSG--QLLGDLDKL-----------SDQTLLGLAPPPPNSPTASESSSISL 368 (470)
T ss_pred cccccccCC-----------CcCCCccccccc--chhhhhccc-----------cchhccccCCCCCCCCCCCccccccc
Confidence 777766332 011111222221 122333333 17899999999999999999999999
Q ss_pred hhhhccCCCCCCCCCCCC
Q 011515 387 FDMFSDATNAPNSINTQP 404 (484)
Q Consensus 387 ~~~~~~~~~~~~~~~~~~ 404 (484)
+|+++......++..+.+
T Consensus 369 ~~~~~~~~s~~s~~~~~~ 386 (470)
T KOG1087|consen 369 LSLSSDNQSELSNSATNS 386 (470)
T ss_pred ccccccccccCCcccccC
Confidence 999988866665444443
No 2
>KOG1086 consensus Cytosolic sorting protein/ADP-ribosylation factor effector GGA [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=6.4e-52 Score=423.69 Aligned_cols=288 Identities=24% Similarity=0.378 Sum_probs=255.0
Q ss_pred hHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchH
Q 011515 2 VNSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKN 81 (484)
Q Consensus 2 v~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~ 81 (484)
++.||.|||++.+.++||..|..|||.||++++++..|+|.+.+||++...+++++||++||+||||||++||.+|++++
T Consensus 9 le~wlnrATdp~~~eedw~ai~~fceqinkdp~gp~lAv~LlaHKiqSPqe~EAl~altvLe~cmkncGekfH~evgkfr 88 (594)
T KOG1086|consen 9 LEYWLNRATDPSNDEEDWKAIDGFCEQINKDPEGPLLAVRLLAHKIQSPQEWEALQALTVLEYCMKNCGEKFHEEVGKFR 88 (594)
T ss_pred HHHHHHhccCccchHHHHHHHHHHHHHHhcCCCCchhHHHHHHhhcCChhHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhccC-----CChhHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHhcCCC--CCCCCCCCCCCCCCC-C
Q 011515 82 VLHEMVKIARKK-----PDTHVKEKILILIDTWQEAFGGPRARYPQYYAAYQELLRAGAVF--PQRSERSAPVFTPPQ-T 153 (484)
Q Consensus 82 FLneLvkLv~~k-----~d~~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~kGi~F--P~~~e~~~piftPp~-~ 153 (484)
|||||+|++++| +...||.||++|+..|+.+|+. .++|+++|++||++||+- |..++...+++.||+ .
T Consensus 89 FLNELIkvvsPKYlG~~tSekvKtkiIelLfsWtv~lpe----~~KikdaYqmLKkqgIik~DP~lp~d~~~~p~ppP~p 164 (594)
T KOG1086|consen 89 FLNELIKVVSPKYLGSRTSEKVKTKIIELLFSWTVSLPE----EPKIKDAYQMLKKQGIIKSDPKLPVDETPVPAPPPRP 164 (594)
T ss_pred HHHHHHHHhCchhcchhhhHHHHHHHHHHHhhheecCcc----cchHHHHHHHHHhcCcccCCCCCCCCCccCCCCCCCC
Confidence 999999999887 3579999999999999999986 589999999999999974 333333356665543 2
Q ss_pred CC----------------CCCCCCCCCCchhhh--HhHhhhcccCCCCCCHHHHHHHHHHHHHHHHHHhhcCCCCCccCc
Q 011515 154 HP----------------LTSYPQNFRNPEHQQ--EAAEASAESEFPTLSLTEIQNARGIMDVLAEMLNALDPNNKEGLR 215 (484)
Q Consensus 154 ~p----------------~Ss~P~~lr~a~~~~--~~~e~~~~~e~~~~~lseLe~ak~nv~LL~EML~~~~P~~~e~~d 215 (484)
.. +|++|+|++.+|++. .+++++.+.++.++|++.|++|++++++|.||+..+..++...-|
T Consensus 165 kssvFddEEksklL~rLLkSn~PeDLqaANkLIK~lVkeee~k~eKiskR~~aleev~n~vk~l~em~l~~s~eg~a~pd 244 (594)
T KOG1086|consen 165 KSSVFDDEEKSKLLARLLKSNHPEDLQAANKLIKTLVKEEEHKLEKISKRVKALEEVNNNVKLLEEMLLDYSQEGNASPD 244 (594)
T ss_pred CccccCcHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCc
Confidence 11 278999999999874 467888888889999999999999999999999999876555567
Q ss_pred hH-HHHHHHHHHHHHHHHHHHHhhcc-CCHHHHHHHhhhhHHHHHHHHHHHhhhcCCccccccCCCCCCCCCCCCccccC
Q 011515 216 QE-VIVDLVDQCRTYKQRVVHLVNST-ADESLLCQGLQLNDDLQRLLAKHESFASGKSAQTAQTDKPKTESKSSEALVDV 293 (484)
Q Consensus 216 ~E-li~EL~~~Cr~~q~rV~rLI~~~-~DEelL~eLL~aNDeL~~vL~rYe~l~~g~~~~~~~~~~~~~~~~~~~~LiD~ 293 (484)
+| +++++|++|.++|+.++||++++ +|++.|+++|++||.|++|+..|+..++|+.+.+..++.+.+ +..+.|||.
T Consensus 245 ~E~~lq~v~~~ce~lr~tlfrlaset~dnD~aL~eILqanD~ltrvi~~ykt~~~G~~~~g~a~t~slp--d~q~~l~~n 322 (594)
T KOG1086|consen 245 NELLLQEVYNRCEQLRPTLFRLASETEDNDPALAEILQANDNLTRVINLYKTPKEGNVANGSARTQSLP--DSQSLLVDN 322 (594)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcccccCcHHHHHHHhhhhhHHhhhhhcccccccccccccceeccCC--cchhheeec
Confidence 77 99999999999999999999987 678999999999999999999999999999987765555555 778899998
Q ss_pred CC
Q 011515 294 DG 295 (484)
Q Consensus 294 ~~ 295 (484)
.|
T Consensus 323 ~P 324 (594)
T KOG1086|consen 323 TP 324 (594)
T ss_pred CC
Confidence 43
No 3
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=100.00 E-value=7.3e-42 Score=312.59 Aligned_cols=137 Identities=29% Similarity=0.564 Sum_probs=132.4
Q ss_pred hHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchH
Q 011515 2 VNSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKN 81 (484)
Q Consensus 2 v~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~ 81 (484)
++.+|+||||+.+.++||+.|++|||+||+++.++++|+|+|+|||+|+|+++|++||+|||+||||||.+||.+|++++
T Consensus 1 ~e~~iekATse~l~~~dw~~il~icD~I~~~~~~~k~a~ral~KRl~~~n~~v~l~AL~LLe~~vkNCG~~fh~evask~ 80 (144)
T cd03568 1 FDDLVEKATDEKLTSENWGLILDVCDKVKSDENGAKDCLKAIMKRLNHKDPNVQLRALTLLDACAENCGKRFHQEVASRD 80 (144)
T ss_pred ChHHHHHHcCccCCCcCHHHHHHHHHHHhcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHhhHH
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhccCCChhHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHhcCCCCC
Q 011515 82 VLHEMVKIARKKPDTHVKEKILILIDTWQEAFGGPRARYPQYYAAYQELLRAGAVFPQ 139 (484)
Q Consensus 82 FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~kGi~FP~ 139 (484)
|+++|+++++++++..||+|||++|+.|+.+|++++ .+..|.++|++|+++|+.||.
T Consensus 81 Fl~eL~kl~~~~~~~~Vk~kil~li~~W~~~f~~~~-~l~~i~~~y~~L~~~G~~f~~ 137 (144)
T cd03568 81 FTQELKKLINDRVHPTVKEKLREVVKQWADEFKNDP-SLSLMSDLYKKLKNEGPDLVT 137 (144)
T ss_pred HHHHHHHHhcccCCHHHHHHHHHHHHHHHHHhCCCc-ccHHHHHHHHHHHHcCCCCCC
Confidence 999999999988999999999999999999999764 699999999999999999984
No 4
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=100.00 E-value=7.2e-42 Score=311.92 Aligned_cols=137 Identities=36% Similarity=0.608 Sum_probs=133.0
Q ss_pred hHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchH
Q 011515 2 VNSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKN 81 (484)
Q Consensus 2 v~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~ 81 (484)
++++|+|||++.+.++||+.|++|||+||+++.+++||+|+|+|||+++|+++|++||+|||+||||||.+||.+|++++
T Consensus 5 ~~~~I~kATs~~l~~~dw~~ileicD~In~~~~~~k~a~ral~krl~~~n~~vql~AL~LLe~~vkNCG~~fh~evas~~ 84 (142)
T cd03569 5 FDELIEKATSELLGEPDLASILEICDMIRSKDVQPKYAMRALKKRLLSKNPNVQLYALLLLESCVKNCGTHFHDEVASRE 84 (142)
T ss_pred HHHHHHHHcCcccCccCHHHHHHHHHHHhCCCCCHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHCCHHHHHHHhhHH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhccCCChhHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHhcCCCCC
Q 011515 82 VLHEMVKIARKKPDTHVKEKILILIDTWQEAFGGPRARYPQYYAAYQELLRAGAVFPQ 139 (484)
Q Consensus 82 FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~kGi~FP~ 139 (484)
|+++|+++++++++..||+|||++|+.|+.+|+++ .+|+.|.++|++|+++||.||+
T Consensus 85 fl~~l~~l~~~~~~~~Vk~kil~li~~W~~~f~~~-~~l~~i~~~y~~L~~~G~~FP~ 141 (142)
T cd03569 85 FMDELKDLIKTTKNEEVRQKILELIQAWALAFRNK-PQLKYVVDTYQILKAEGHKFPE 141 (142)
T ss_pred HHHHHHHHHcccCCHHHHHHHHHHHHHHHHHhCCC-cccHHHHHHHHHHHHcCCCCCC
Confidence 99999999998899999999999999999999986 4799999999999999999995
No 5
>cd03565 VHS_Tom1 VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. The VHS domain of the Tom1 protein is essential for the negative regulation of Interleukin-1 and Tumor Necrosis Factor-induced signaling pathways.
Probab=100.00 E-value=2.1e-41 Score=308.58 Aligned_cols=136 Identities=40% Similarity=0.756 Sum_probs=129.7
Q ss_pred hHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHHHhcccchhhhhhcch
Q 011515 2 VNSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRIGS-RNSKVQLLALTLLETIIKNCGDIVHMHVAEK 80 (484)
Q Consensus 2 v~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL~s-~np~vqllAL~LLE~cVKNCG~~Fh~eVask 80 (484)
|+.+|+||||+.++++||+.|++|||+||++..++++|+|+|+|||++ +|+++|++||+|||+||||||.+||.+|+++
T Consensus 2 ~~~~IekATse~l~~~dw~~ileicD~In~~~~~~k~a~ralkkRl~~~~n~~v~l~aL~LLe~~vkNCG~~fh~eiask 81 (141)
T cd03565 2 VGQLIEKATDGSLQSEDWGLNMEICDIINETEDGPKDAVRALKKRLNGNKNHKEVMLTLTVLETCVKNCGHRFHVLVAKK 81 (141)
T ss_pred HhHHHHHHcCcCCCCcCHHHHHHHHHHHhCCCCcHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHccHHHHHHHHHH
Confidence 689999999999999999999999999999999999999999999985 7999999999999999999999999999999
Q ss_pred HHHHH-HHHHhccC--CChhHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHhcCCCC
Q 011515 81 NVLHE-MVKIARKK--PDTHVKEKILILIDTWQEAFGGPRARYPQYYAAYQELLRAGAVFP 138 (484)
Q Consensus 81 ~FLne-LvkLv~~k--~d~~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~kGi~FP 138 (484)
+|+++ |++++.++ ++..||+|||++|+.|+.+|++++ +|+.|.++|++|+++||.||
T Consensus 82 ~Fl~e~L~~~i~~~~~~~~~Vk~kil~li~~W~~~f~~~~-~l~~i~~~y~~L~~~G~~FP 141 (141)
T cd03565 82 DFIKDVLVKLINPKNNPPTIVQEKVLALIQAWADAFRGSP-DLTGVVEVYEELKKKGIEFP 141 (141)
T ss_pred HhhhHHHHHHHcccCCCcHHHHHHHHHHHHHHHHHhCCCc-cchHHHHHHHHHHHcCCCCC
Confidence 99999 99999754 457999999999999999999875 69999999999999999998
No 6
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=100.00 E-value=7.6e-41 Score=304.16 Aligned_cols=131 Identities=28% Similarity=0.501 Sum_probs=125.5
Q ss_pred hHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchH
Q 011515 2 VNSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKN 81 (484)
Q Consensus 2 v~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~ 81 (484)
++++|+||||+.+.++||++|++|||+||+++.++++|+|+|+|||+|+|+++|++||+|||+||||||.+||.+|++++
T Consensus 2 ~~~~iekAT~~~l~~~dw~~ileicD~In~~~~~~k~a~rai~krl~~~n~~v~l~AL~LLe~~vkNCG~~fh~evas~~ 81 (139)
T cd03567 2 LEAWLNKATNPSNREEDWEAIQAFCEQINKEPEGPQLAVRLLAHKIQSPQEKEALQALTVLEACMKNCGERFHSEVGKFR 81 (139)
T ss_pred HHHHHHHHcCccCCCCCHHHHHHHHHHHHcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCHHHHHHHHhHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcc-----CCChhHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHhcCC
Q 011515 82 VLHEMVKIARK-----KPDTHVKEKILILIDTWQEAFGGPRARYPQYYAAYQELLRAGAV 136 (484)
Q Consensus 82 FLneLvkLv~~-----k~d~~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~kGi~ 136 (484)
|+++|++++++ .++..||+|||+||+.|+++|+. .|.|.++|++||++|++
T Consensus 82 Fl~el~kl~~~k~~~~~~~~~Vk~kil~li~~W~~~f~~----~p~~~~~Y~~Lk~~G~i 137 (139)
T cd03567 82 FLNELIKLVSPKYLGSRTSEKVKTKIIELLYSWTLELPH----EPKIKEAYDMLKKQGII 137 (139)
T ss_pred HHHHHHHHhccccCCCCCCHHHHHHHHHHHHHHHHHhcc----cchHHHHHHHHHHCCCc
Confidence 99999999975 36789999999999999999984 57899999999999975
No 7
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=100.00 E-value=1.8e-38 Score=286.37 Aligned_cols=132 Identities=42% Similarity=0.723 Sum_probs=126.5
Q ss_pred hHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchH
Q 011515 2 VNSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKN 81 (484)
Q Consensus 2 v~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~ 81 (484)
++.+|++|||+.+.++||+.|++|||+||+++.++++|+|+|+|||+++|+++|++||+|||+||||||.+||.+|++++
T Consensus 1 ~~~~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 1 VERLIDKATSPSLLEEDWELILEICDLINSTPDGPKDAVRLLKKRLNNKNPHVALLALTLLDACVKNCGSKFHLEVASKE 80 (133)
T ss_pred ChhHHHHHcCcCCCCcCHHHHHHHHHHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHhHH
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhccCCChh-HHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHhc
Q 011515 82 VLHEMVKIARKKPDTH-VKEKILILIDTWQEAFGGPRARYPQYYAAYQELLRAG 134 (484)
Q Consensus 82 FLneLvkLv~~k~d~~-VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~kG 134 (484)
|+++|+++++.+++.. ||+||+++|+.|+.+|++++ .|+.|.++|++|+++|
T Consensus 81 fl~~L~~l~~~~~~~~~Vk~kil~li~~W~~~f~~~~-~~~~i~~~y~~L~~~g 133 (133)
T smart00288 81 FLNELVKLIKPKYPLPLVKKRILELIQEWADAFKNDP-DLSQIVDVYDLLKKKG 133 (133)
T ss_pred HHHHHHHHHcCCCCcHHHHHHHHHHHHHHHHHHcCCC-CchHHHHHHHHHHHCc
Confidence 9999999999876655 99999999999999999864 6999999999999988
No 8
>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM. Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....
Probab=100.00 E-value=4.5e-37 Score=278.97 Aligned_cols=132 Identities=42% Similarity=0.756 Sum_probs=122.7
Q ss_pred hHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchH
Q 011515 2 VNSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKN 81 (484)
Q Consensus 2 v~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~ 81 (484)
++.+|++||++.+.++||+.|++|||+||+++.++++|+|+|+|||+|+|+++|++||+|||+||||||..||.+|++++
T Consensus 6 ~~~li~kATs~~~~~~Dw~~~l~icD~i~~~~~~~kea~~~l~krl~~~~~~vq~~aL~lld~lvkNcg~~f~~ev~~~~ 85 (140)
T PF00790_consen 6 ITELIEKATSESLPSPDWSLILEICDLINSSPDGAKEAARALRKRLKHGNPNVQLLALTLLDALVKNCGPRFHREVASKE 85 (140)
T ss_dssp HHHHHHHHT-TTSSS--HHHHHHHHHHHHTSTTHHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHSHHHHHHHHTSHH
T ss_pred HHHHHHHHhCcCCCCCCHHHHHHHHHHHHcCCccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHcCCHHHHHHHhHHH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhccCCChh---HHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHhc
Q 011515 82 VLHEMVKIARKKPDTH---VKEKILILIDTWQEAFGGPRARYPQYYAAYQELLRAG 134 (484)
Q Consensus 82 FLneLvkLv~~k~d~~---VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~kG 134 (484)
|+++|+++++.+.... ||+|++++|+.|+.+|+++ +.|+.|.++|++||++|
T Consensus 86 fl~~l~~l~~~~~~~~~~~Vk~k~l~ll~~W~~~f~~~-~~~~~i~~~y~~Lk~~G 140 (140)
T PF00790_consen 86 FLDELVKLIKSKKTDPETPVKEKILELLQEWAEAFKSD-PELSLIQDTYKRLKRKG 140 (140)
T ss_dssp HHHHHHHHHHHTTTHHHSHHHHHHHHHHHHHHHHTTTS-TTGHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHccCCCCchhHHHHHHHHHHHHHHHHHCCC-CCchHHHHHHHHHHHCc
Confidence 9999999998765443 9999999999999999776 46999999999999998
No 9
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=100.00 E-value=6.2e-37 Score=275.92 Aligned_cols=131 Identities=49% Similarity=0.807 Sum_probs=125.5
Q ss_pred hHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchH
Q 011515 2 VNSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKN 81 (484)
Q Consensus 2 v~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~ 81 (484)
|+++|++||++.+.++||+.|++|||+||.++.++++|+|+|+|||+++|+++|++||+|||+||||||.+||.+|++++
T Consensus 1 v~~~I~kATs~~~~~~D~~~il~icd~I~~~~~~~k~a~raL~krl~~~n~~vql~AL~lLd~~vkNcg~~f~~~i~s~~ 80 (133)
T cd03561 1 VTSLIERATSPSLEEPDWALNLELCDLINLKPNGPKEAARAIRKKIKYGNPHVQLLALTLLELLVKNCGKPFHLQVADKE 80 (133)
T ss_pred ChHHHHHHcCcccCCccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCChHHHHHHhhHH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcc--CCChhHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHH
Q 011515 82 VLHEMVKIARK--KPDTHVKEKILILIDTWQEAFGGPRARYPQYYAAYQELLR 132 (484)
Q Consensus 82 FLneLvkLv~~--k~d~~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~ 132 (484)
||++|++++.+ +++..||+||+++|+.|+.+|+++..+++.|.++|++||+
T Consensus 81 fl~~l~~l~~~~~~~~~~Vk~kil~ll~~W~~~f~~~~~~~~~~~~~y~~lk~ 133 (133)
T cd03561 81 FLLELVKIAKNSPKYDPKVREKALELILAWSESFGGHSEDLPGIEDAYKLLKR 133 (133)
T ss_pred HHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHhcCCCccchHHHHHHHHHhC
Confidence 99999999986 6889999999999999999999864579999999999984
No 10
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=100.00 E-value=1.8e-34 Score=293.63 Aligned_cols=265 Identities=24% Similarity=0.376 Sum_probs=199.7
Q ss_pred hHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchH
Q 011515 2 VNSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKN 81 (484)
Q Consensus 2 v~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~ 81 (484)
++.+|+|||++.++.+||++||.|||+|+++++++|+++|+|+|||.++++||+|+||+||++|++|||++||++|++++
T Consensus 9 ~e~~v~KAT~e~nT~enW~~IlDvCD~v~~~~~~~kd~lk~i~KRln~~dphV~L~AlTLlda~~~NCg~~~r~EVsSr~ 88 (462)
T KOG2199|consen 9 FEQDVEKATDEKNTSENWSLILDVCDKVGSDPDGGKDCLKAIMKRLNHKDPHVVLQALTLLDACVANCGKRFRLEVSSRD 88 (462)
T ss_pred HHHHHHHhcCcccccccHHHHHHHHHhhcCCCcccHHHHHHHHHHhcCCCcchHHHHHHHHHHHHHhcchHHHHHHhhhh
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhccCCChhHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHhcCCCCCCCCCC--CCCCC----C-----
Q 011515 82 VLHEMVKIARKKPDTHVKEKILILIDTWQEAFGGPRARYPQYYAAYQELLRAGAVFPQRSERS--APVFT----P----- 150 (484)
Q Consensus 82 FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~kGi~FP~~~e~~--~pift----P----- 150 (484)
|.++|.+|+..+.+..|++|+..++..|++.|+.++ .+..|.++|+.||+.||.|+..+.-. ..+-+ .
T Consensus 89 F~~el~al~~~~~h~kV~~k~~~lv~eWsee~K~Dp-~lsLi~~l~~klk~~g~~f~~~~~k~~k~a~~~~~v~~k~EeE 167 (462)
T KOG2199|consen 89 FTTELRALIESKAHPKVCEKMRDLVKEWSEEFKKDP-SLSLISALYKKLKEEGITFLVAGSKPEKHAMSTNTVSSKQEEE 167 (462)
T ss_pred HHHHHHHHHhhcccHHHHHHHHHHHHHHHHHhccCc-chhHHHHHHHHHHHcCCCcccCCCchhHHHhhcccccccccHH
Confidence 999999999988999999999999999999999986 58999999999999999998643210 00000 0
Q ss_pred ---------------C----CCCCCCCCCCC----------CCC--------chhhhHhHhhhccc--------------
Q 011515 151 ---------------P----QTHPLTSYPQN----------FRN--------PEHQQEAAEASAES-------------- 179 (484)
Q Consensus 151 ---------------p----~~~p~Ss~P~~----------lr~--------a~~~~~~~e~~~~~-------------- 179 (484)
. .+...+-||.. +.+ +-+..++.++....
T Consensus 168 diaKAi~lSL~E~~~Q~k~a~~~tst~yPs~qk~nqapa~~l~s~~~~rkVRALYDFeAaE~nELsFkaGdIItVLd~s~ 247 (462)
T KOG2199|consen 168 DIAKAIELSLKEQEKQKKLAETETSTLYPSHQKQNQAPASQLNSQTVVRKVRALYDFEAAEDNELSFKAGDIITVLDDSD 247 (462)
T ss_pred HHHHHHHhhHHHHhhchhhccCCccccCccccccccCchhhccCCccchhhhhhhcccccCCCccceecCcEEEEcccCC
Confidence 0 00001112210 000 00000111100000
Q ss_pred -----------------CCCC-----CCHHHHH-----------HHHHHHHHHHHHHhhcCCCCCccCchHHHHHHHHHH
Q 011515 180 -----------------EFPT-----LSLTEIQ-----------NARGIMDVLAEMLNALDPNNKEGLRQEVIVDLVDQC 226 (484)
Q Consensus 180 -----------------e~~~-----~~lseLe-----------~ak~nv~LL~EML~~~~P~~~e~~d~Eli~EL~~~C 226 (484)
.+.+ ....+++ .....++-|-.+|.+.+|.+... |++-|.+|+..|
T Consensus 248 ~~WWKG~~~~~~GlFPsnfVT~~le~~~~ee~~~~~~~~E~~vfi~e~~iDrlL~~L~~~dPtd~~~-D~~~l~~le~~~ 326 (462)
T KOG2199|consen 248 PNWWKGENHRGIGLFPSNFVTADLEEPKIEEQEQKQKNKEAIVFIDEDKIDRLLQVLHEADPTDEVQ-DDDDLLDLEAAV 326 (462)
T ss_pred cchhccccCCcccccchhhhhhhhcccchhhhhhhhcCcceeeeccHHHHHHHHHHHhhcCCCCccC-CCHHHHHHHHHH
Confidence 0000 0011111 12345666778899999976554 555567899999
Q ss_pred HHHHHHHHHHhhccCCHHHHHHHhhhhHHHHHHHHHHHhhhcCC
Q 011515 227 RTYKQRVVHLVNSTADESLLCQGLQLNDDLQRLLAKHESFASGK 270 (484)
Q Consensus 227 r~~q~rV~rLI~~~~DEelL~eLL~aNDeL~~vL~rYe~l~~g~ 270 (484)
..|++.|-+.++.++-+ =++|+++|..|..|+..|+++....
T Consensus 327 ~~mgPlid~~Le~idrk--~~eL~~Ln~~l~~Al~lY~kLm~~~ 368 (462)
T KOG2199|consen 327 HQMGPLIDRKLEKIDRK--HEELSQLNVKLLDALRLYNKLMNEA 368 (462)
T ss_pred HHhhhHHHHHHHHHHhh--HHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 99999999999988543 2467889999999999999987655
No 11
>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=99.93 E-value=2.3e-25 Score=195.07 Aligned_cols=109 Identities=40% Similarity=0.708 Sum_probs=102.1
Q ss_pred hHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchH
Q 011515 2 VNSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKN 81 (484)
Q Consensus 2 v~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~ 81 (484)
++.+|++||++.+.+|||..+++|||+++..+.++++++++|+|||+++|+++++.||.|||+||||||++||.+|+++.
T Consensus 1 ~~~~v~~AT~~~~~~p~~~~i~~i~d~~~~~~~~~~~~~~~l~kRl~~~~~~~~lkaL~lLe~lvkN~g~~f~~~i~~~~ 80 (115)
T cd00197 1 FEKTVEKATSNENMGPDWPLIMEICDLINETNVGPKEAVDAIKKRINNKNPHVVLKALTLLEYCVKNCGERFHQEVASND 80 (115)
T ss_pred ChHHHHHHcCCCCCCCCHHHHHHHHHHHHCCCccHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHccHHHHHHHHHhH
Confidence 36899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhc-----cCCChhHHHHHHHHHHHHH
Q 011515 82 VLHEMVKIAR-----KKPDTHVKEKILILIDTWQ 110 (484)
Q Consensus 82 FLneLvkLv~-----~k~d~~VkeKiLeLIq~Wa 110 (484)
|+.+|.+... ...+..||+|+++|++.|+
T Consensus 81 ~~~~l~~~~~~~~~~~~~~~~Vr~k~~~l~~~w~ 114 (115)
T cd00197 81 FAVELLKFDKSKLLGDDVSTNVREKAIELVQLWA 114 (115)
T ss_pred HHHHHHHhhccccccCCCChHHHHHHHHHHHHHh
Confidence 9999987522 2357899999999999997
No 12
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=99.88 E-value=4.8e-23 Score=222.57 Aligned_cols=144 Identities=35% Similarity=0.616 Sum_probs=136.1
Q ss_pred HHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHH
Q 011515 3 NSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNV 82 (484)
Q Consensus 3 ~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~F 82 (484)
..+|++||++.+-+.||..|++|||+|++....+|+++|.|+|||.|.|+++++.+|.|+|.||||||..||.+|++++|
T Consensus 10 ~~l~~~at~~~~~~~~~e~~~e~~d~ir~~~~~~k~slr~~~~~i~h~np~~~~~~~~~~d~cvkn~G~gv~~ei~tre~ 89 (634)
T KOG1818|consen 10 KRLIEKATSETLGSGDWEAILEISDMIRSGGVPPKPSLRGIKKRIDHENPNVQLFTLKLTDHCVKNCGHGVHCEIATREF 89 (634)
T ss_pred HhhhhhhhhhhhcCcchhhhhhHHHHHHhcCCCCchhHHHHHHHHhccCCCcccchhhhHHHHHhcCCcchhHHHHHHHH
Confidence 56899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhccC-CChhHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHhcCCCCCCCCCCCCCC
Q 011515 83 LHEMVKIARKK-PDTHVKEKILILIDTWQEAFGGPRARYPQYYAAYQELLRAGAVFPQRSERSAPVF 148 (484)
Q Consensus 83 LneLvkLv~~k-~d~~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~kGi~FP~~~e~~~pif 148 (484)
|+.|..++... .+..|+.|+|++|+.|+.+|++. +.|..+.++|+.||..|++||+.++.++ +|
T Consensus 90 m~~~~~~l~~~~~~e~v~~~~l~~~q~wa~af~~~-~~~~~v~~t~~~lk~~g~~Fpe~~e~d~-mf 154 (634)
T KOG1818|consen 90 MDLLKSLLESQRIHEEVKNKILELIQNWAAAFRNS-SKYSYVLDTYQKLKGGGHVFPELDENDA-MF 154 (634)
T ss_pred HHHHHhhhccccccchHHHHHHHHHHHHHHHccCc-hHHHHHHHHHHHHhcCCccccccccchh-hh
Confidence 99999999764 88999999999999999999987 6799999999999999999999876553 55
No 13
>PF03127 GAT: GAT domain; InterPro: IPR004152 The GAT domain is responsible for binding of GGA proteins to several members of the ARF family including ARF1 [] and ARF3. The GAT domain stabilises membrane bound ARF1 in its GTP bound state, by interfering with GAP proteins [].; GO: 0006886 intracellular protein transport, 0005622 intracellular; PDB: 1YD8_H 1WR6_C 1WRD_A 1O3X_A 1J2J_B 1NWM_X 1X79_A 1OXZ_A 1NAF_A.
Probab=99.83 E-value=7.9e-21 Score=163.60 Aligned_cols=94 Identities=27% Similarity=0.498 Sum_probs=85.6
Q ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHhhcCCCCCccCchHHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHhhhhHHHHH
Q 011515 179 SEFPTLSLTEIQNARGIMDVLAEMLNALDPNNKEGLRQEVIVDLVDQCRTYKQRVVHLVNSTADESLLCQGLQLNDDLQR 258 (484)
Q Consensus 179 ~e~~~~~lseLe~ak~nv~LL~EML~~~~P~~~e~~d~Eli~EL~~~Cr~~q~rV~rLI~~~~DEelL~eLL~aNDeL~~ 258 (484)
+++.+++.++|+.|+++++||+|||+.++|++....+.|+++|||++||+||++|++||+.+.||++|++||++||+|++
T Consensus 3 ~e~~~k~~~~l~~v~~~~~lL~emL~~~~~~~~~~~~~el~~eL~~~ck~~r~~i~~li~~~~dee~l~~lL~~ND~L~~ 82 (100)
T PF03127_consen 3 PEQVSKRRSELEKVKNNAKLLNEMLDNYDPGEESSSDNELIQELYESCKSMRPRIQRLIEEVEDEELLGELLQANDELNQ 82 (100)
T ss_dssp HCTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTSTHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHHH
Confidence 44555667899999999999999999999998877777999999999999999999999999888899999999999999
Q ss_pred HHHHHHhhhcCCcc
Q 011515 259 LLAKHESFASGKSA 272 (484)
Q Consensus 259 vL~rYe~l~~g~~~ 272 (484)
||.+|+++++|+..
T Consensus 83 ~l~~Y~~l~~~~~~ 96 (100)
T PF03127_consen 83 ALERYDRLVKGQQR 96 (100)
T ss_dssp HHHHHHHHHCCC--
T ss_pred HHHHHHHHHcCccc
Confidence 99999999999875
No 14
>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=98.10 E-value=3.1e-05 Score=69.63 Aligned_cols=106 Identities=20% Similarity=0.266 Sum_probs=85.7
Q ss_pred ChHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcch
Q 011515 1 MVNSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEK 80 (484)
Q Consensus 1 ~v~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask 80 (484)
|-..+|.+||++.-..+--...-|||.+...+.....+.+..|-|||++++++|-+-||.+|+.|+.++...|.+++...
T Consensus 1 ~~~~ll~~ATsdd~~p~pgy~~~Eia~~t~~s~~~~~ei~d~L~kRL~~~~~hVK~K~Lrilk~l~~~G~~~f~~~~~~~ 80 (122)
T cd03572 1 MRRSLLSKATSDDDEPTPGYLYEEIAKLTRKSVGSCQELLEYLLKRLKRSSPHVKLKVLKIIKHLCEKGNSDFKRELQRN 80 (122)
T ss_pred CcHHHHHHHhcCCCCCCchHHHHHHHHHHHcCHHHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHHhhCCHHHHHHHHHh
Confidence 44679999999988887777888999999999889999999999999999999999999999999999998998877543
Q ss_pred HHHHHHHHHhcc-C-CC--------hhHHHHHHHHHHH
Q 011515 81 NVLHEMVKIARK-K-PD--------THVKEKILILIDT 108 (484)
Q Consensus 81 ~FLneLvkLv~~-k-~d--------~~VkeKiLeLIq~ 108 (484)
...+..+..- . +| ..||+++.+++..
T Consensus 81 --~~~Ik~~~~f~g~~Dp~~Gd~~~~~VR~~A~El~~~ 116 (122)
T cd03572 81 --SAQIRECANYKGPPDPLKGDSLNEKVREEAQELIKA 116 (122)
T ss_pred --HHHHHHHHHcCCCCCcccCcchhHHHHHHHHHHHHH
Confidence 3334433321 1 22 3688888777654
No 15
>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=98.08 E-value=3e-05 Score=69.18 Aligned_cols=105 Identities=23% Similarity=0.299 Sum_probs=80.1
Q ss_pred hHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHHHhcccchhhhhhc
Q 011515 2 VNSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRI---GSRNSKVQLLALTLLETIIKNCGDIVHMHVA 78 (484)
Q Consensus 2 v~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL---~s~np~vqllAL~LLE~cVKNCG~~Fh~eVa 78 (484)
++.+|.+||+..--++.-..+.+||..-... ....+.+..|.||| ..++.++.+-||.||+.|++||...|-.++-
T Consensus 4 ~e~~v~eAT~~d~~gp~~~~l~eIa~~t~~~-~~~~~I~~~l~kRL~~~~~k~wr~~~KaL~ll~yLl~nG~~~~~~~~~ 82 (125)
T PF01417_consen 4 LELKVREATSNDPWGPPGKLLAEIAQLTYNS-KDCQEIMDVLWKRLSKSDGKNWRHVYKALTLLEYLLKNGSERFVDELR 82 (125)
T ss_dssp HHHHHHHHTSSSSSS--HHHHHHHHHHTTSC-HHHHHHHHHHHHHHHSSTSSGHHHHHHHHHHHHHHHHHS-HHHHHHHH
T ss_pred HHHHHHHHcCCCCCCcCHHHHHHHHHHHhcc-ccHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHHHHHHCCHHHHHHHH
Confidence 4678999999988788777888888887666 78999999999999 7889999999999999999999999888773
Q ss_pred chHHHHHHHHHhc-----cC-CC--hhHHHHHHHHHHHH
Q 011515 79 EKNVLHEMVKIAR-----KK-PD--THVKEKILILIDTW 109 (484)
Q Consensus 79 sk~FLneLvkLv~-----~k-~d--~~VkeKiLeLIq~W 109 (484)
+-+..+..+.. ++ .+ ..||+|+-+++...
T Consensus 83 --~~~~~I~~l~~f~~~d~~g~d~~~~VR~~A~~i~~lL 119 (125)
T PF01417_consen 83 --DHIDIIRELQDFQYVDPKGKDQGQNVREKAKEILELL 119 (125)
T ss_dssp --HTHHHHHGGGG---BBTTSTBHHHHHHHHHHHHHHHH
T ss_pred --HHHHHHhhcceeeccCCCCccHHHHHHHHHHHHHHHh
Confidence 33444444422 11 11 25998888887654
No 16
>cd03562 CID CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1. Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.
Probab=97.85 E-value=4.9e-05 Score=66.43 Aligned_cols=94 Identities=23% Similarity=0.342 Sum_probs=75.3
Q ss_pred CHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhccCCChh
Q 011515 18 DWAMNIEICDMLNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTH 97 (484)
Q Consensus 18 Dw~~ileICD~In~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~ 97 (484)
.-..|-.+...+......+++.+.+|.++|+...+...|.+|.|+|.+++|||.+....+.. .|.+-+..... +.+..
T Consensus 17 S~~~I~~lt~~a~~~~~~a~~iv~~i~~~i~~~~~~~KL~~LYL~dsIvkn~~~~~~~~~~~-~~~~~f~~~~~-~~~~~ 94 (114)
T cd03562 17 SQPSIQTLTKLAIENRKHAKEIVEIIEKHIKKCPPEQKLPLLYLLDSIVKNVGRKYKEFFSE-FLVPLFLDAYE-KVDEK 94 (114)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccchHHHHHHHHHHHHcccchHHHHHH-HHHHHHHHHHH-hCCHH
Confidence 44566667777776667889999999999999999999999999999999999987766553 23333433333 67899
Q ss_pred HHHHHHHHHHHHHHHh
Q 011515 98 VKEKILILIDTWQEAF 113 (484)
Q Consensus 98 VkeKiLeLIq~Wa~aF 113 (484)
+|+|+..|+..|.+.+
T Consensus 95 ~r~kl~rl~~iW~~~~ 110 (114)
T cd03562 95 TRKKLERLLNIWEERF 110 (114)
T ss_pred HHHHHHHHHHHccCCC
Confidence 9999999999999765
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=97.64 E-value=0.00064 Score=61.22 Aligned_cols=106 Identities=25% Similarity=0.263 Sum_probs=81.3
Q ss_pred hHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCC--CCHHHHHHHHHHHHHHHhcccchhhhhhcc
Q 011515 2 VNSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRIGS--RNSKVQLLALTLLETIIKNCGDIVHMHVAE 79 (484)
Q Consensus 2 v~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL~s--~np~vqllAL~LLE~cVKNCG~~Fh~eVas 79 (484)
.+.+|..|||...-+|.=..+-+||+.-.. .....+.+..|.|||.. ++-+.++-||+|||.|++|+..+|-.++.+
T Consensus 2 ~e~~vreATs~d~wGp~~~~m~eIa~~t~~-~~~~~~Im~~l~kRL~~~~k~WR~vyKaL~lleyLl~nGse~vv~~~r~ 80 (123)
T cd03571 2 AELKVREATSNDPWGPSGTLMAEIARATYN-YVEFQEIMSMLWKRLNDKGKNWRHVYKALTLLEYLLKNGSERVVDDARE 80 (123)
T ss_pred HHHHHHHHcCCCCCCCCHHHHHHHHHHhCC-HHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHhCCHHHHHHHHH
Confidence 467899999998888888889999988554 45678999999999964 589999999999999999999988877743
Q ss_pred hHHHHHHHHHh-----ccC-CC--hhHHHHHHHHHHHHH
Q 011515 80 KNVLHEMVKIA-----RKK-PD--THVKEKILILIDTWQ 110 (484)
Q Consensus 80 k~FLneLvkLv-----~~k-~d--~~VkeKiLeLIq~Wa 110 (484)
-+..|..|- ..+ .| ..||+|+..++....
T Consensus 81 --~~~~i~~L~~F~~~d~~g~d~G~~VR~ka~~i~~Ll~ 117 (123)
T cd03571 81 --NLYIIRTLKDFQYIDENGKDQGINVREKAKEILELLE 117 (123)
T ss_pred --hHHHHHhhccceeeCCCCCchhHHHHHHHHHHHHHhC
Confidence 333333332 111 12 479999888876544
No 18
>smart00273 ENTH Epsin N-terminal homology (ENTH) domain.
Probab=97.61 E-value=0.00091 Score=59.74 Aligned_cols=108 Identities=17% Similarity=0.235 Sum_probs=81.1
Q ss_pred hHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHhcccchhhhhhcch
Q 011515 2 VNSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRIGSR-NSKVQLLALTLLETIIKNCGDIVHMHVAEK 80 (484)
Q Consensus 2 v~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL~s~-np~vqllAL~LLE~cVKNCG~~Fh~eVask 80 (484)
++..|.+||+.....|.-..+-+|+......+....+.+.+|.+||... +..+++-||.||+.|++|+...|-.++-+.
T Consensus 3 ~e~~V~kAT~~~~~~p~~k~~~~I~~~t~~~~~~~~~i~~~l~~Rl~~~~~w~~v~KsL~llh~ll~~G~~~~~~~~~~~ 82 (127)
T smart00273 3 LEVKVRKATNNDEWGPKGKHLREIIQGTHNEKSSFAEIMAVLWRRLNDTKNWRVVYKALILLHYLLRNGSPRVILEALRN 82 (127)
T ss_pred HHHHHHHhcCCCCCCcCHHHHHHHHHHHccCHhhHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHhcCCHHHHHHHHHh
Confidence 4678999999999999999999999999888788999999999999765 999999999999999999987665444322
Q ss_pred -HHHHHHHHHhc--cC---CChhHHHHHHHHHHHH
Q 011515 81 -NVLHEMVKIAR--KK---PDTHVKEKILILIDTW 109 (484)
Q Consensus 81 -~FLneLvkLv~--~k---~d~~VkeKiLeLIq~W 109 (484)
..+..|...-. .. ...-||+++..|+..-
T Consensus 83 ~~~i~~L~~f~~~~~~~~d~g~~VR~ya~~L~~~l 117 (127)
T smart00273 83 RNRILNLSDFQDIDSRGKDQGANIRTYAKYLLERL 117 (127)
T ss_pred hHHHhhHhhCeecCCCCeeCcHHHHHHHHHHHHHH
Confidence 12222333211 11 1235777776666543
No 19
>cd03564 ANTH_AP180_CALM ANTH domain family; composed of adaptor protein 180 (AP180), clathrin assembly lymphoid myeloid leukemia protein (CALM) and similar proteins. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. AP180 and CALM play important roles in clathrin-mediated endocytosis. AP180 is a brain-specific clathrin-binding protein which stimulates clathrin assembly during the recycling of synaptic vesicles. The ANTH domain is structurally similar to the VHS domain and is composed of a superhelix of eight alpha helices. ANTH domains bind both inositol phospholipids and proteins, and contribute to the nucleation and formation of clathrin coats on membranes. ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that the ANTH domain is a universal component of the machine
Probab=97.34 E-value=0.0013 Score=58.21 Aligned_cols=78 Identities=21% Similarity=0.195 Sum_probs=70.8
Q ss_pred hHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcc
Q 011515 2 VNSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAE 79 (484)
Q Consensus 2 v~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVas 79 (484)
++..|.|||+.....|+-..+-+|......+.....+.+.+|.+|+..+|..+++-||.||..|++++...|-.++..
T Consensus 1 ~~~aV~kAT~~~~~~pk~k~v~~ii~~t~~~~~~~~~~~~~l~~Rl~~~~w~v~~K~LillH~llr~G~~~~~~~~~~ 78 (117)
T cd03564 1 LEKAVKKATSHDEAPPKDKHVRKIIAGTSSSPASIPSFASALSRRLLDRNWVVVLKALILLHRLLREGHPSFLQELLS 78 (117)
T ss_pred CchHHHhhcCCCCCCCChHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCcHHHHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence 357899999999999999999999999888788999999999999999999999999999999999998887766654
No 20
>KOG2056 consensus Equilibrative nucleoside transporter protein [Nucleotide transport and metabolism]
Probab=96.75 E-value=0.01 Score=61.74 Aligned_cols=109 Identities=24% Similarity=0.215 Sum_probs=82.6
Q ss_pred HHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHHHhcccchhhhhhcch
Q 011515 3 NSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRIG--SRNSKVQLLALTLLETIIKNCGDIVHMHVAEK 80 (484)
Q Consensus 3 ~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL~--s~np~vqllAL~LLE~cVKNCG~~Fh~eVask 80 (484)
+..|-.||+...-+|.-.++.+|++.--. ...-.+.+-.|.||+. .+|=+.++-||+|||.||+|+.++|-.++-.-
T Consensus 23 e~kVrdAT~nd~wGPs~~lm~eIA~~ty~-~~e~~eIm~vi~kRl~d~gknWR~VyKaLtlleyLl~~GSErv~~~~ren 101 (336)
T KOG2056|consen 23 ELKVRDATSNDPWGPSGTLMAEIAQATYN-FVEYQEIMDVLWKRLNDSGKNWRHVYKALTLLEYLLKNGSERVVDETREN 101 (336)
T ss_pred HHHHHhccccccCCCchHHHHHHHHHhcC-HHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHhcCcHHHHHHHHhh
Confidence 45788999999999999999999986433 3457899999999995 47889999999999999999988877666544
Q ss_pred HHHHHHHHHh---c-cCC--ChhHHHHHHHHHHHHHHH
Q 011515 81 NVLHEMVKIA---R-KKP--DTHVKEKILILIDTWQEA 112 (484)
Q Consensus 81 ~FLneLvkLv---~-~k~--d~~VkeKiLeLIq~Wa~a 112 (484)
-++-++.+=+ . ... -..||+|+-+++....+.
T Consensus 102 ~~~I~tL~~Fq~iD~~G~dqG~nVRkkak~l~~LL~D~ 139 (336)
T KOG2056|consen 102 IYTIETLKDFQYIDEDGKDQGLNVRKKAKELLSLLEDD 139 (336)
T ss_pred hHHHHHHhhceeeCCCCccchHHHHHHHHHHHHHhccH
Confidence 4444433222 1 111 247999999999887754
No 21
>KOG2374 consensus Uncharacterized conserved protein [Function unknown]
Probab=96.70 E-value=0.015 Score=62.81 Aligned_cols=135 Identities=14% Similarity=0.268 Sum_probs=109.5
Q ss_pred hHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcc--
Q 011515 2 VNSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAE-- 79 (484)
Q Consensus 2 v~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVas-- 79 (484)
|..+|+++|...-.+-|--...+|--+|+.+.+...-+.+.|..-+.+.-..+-+++|-++|.|.-.. +-|...|-+
T Consensus 8 l~~lIeelT~sg~~~~~p~~~k~lkkiv~~sdee~~~~~~~L~~~~~~~h~~vR~l~lqii~elF~rs-~~FR~lii~n~ 86 (661)
T KOG2374|consen 8 LIGLIEELTKSGAQEVDPRLLKALKKIVRYSDEEVRLSSQTLMELMRHNHSQVRYLTLQIIDELFMRS-KLFRTLIIENL 86 (661)
T ss_pred HHHHHHHHhhcCCcccChHHHHHHHHHHhccHHHHHHHHHHHHHHHhhcCchHHHHHHHHHHHHHHhh-HHHHHHHHhCH
Confidence 45799999999999888888899999999888889999999999999888999999999999999877 567776654
Q ss_pred hHHHHHHHHHhccC--C-C----hhHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHH-hcCCCCCC
Q 011515 80 KNVLHEMVKIARKK--P-D----THVKEKILILIDTWQEAFGGPRARYPQYYAAYQELLR-AGAVFPQR 140 (484)
Q Consensus 80 k~FLneLvkLv~~k--~-d----~~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~-kGi~FP~~ 140 (484)
.+||+-+...-... + + ..+|.+.++.|..|.+.|+-+ |..+.=.|..||. +-+.||..
T Consensus 87 ~efLeL~~gt~p~~PLP~p~~~a~~Lr~~ai~~~e~Wnekfg~~---yk~l~lg~~~Lk~tkkvdf~d~ 152 (661)
T KOG2374|consen 87 DEFLELSIGTRPNLPLPAPPAVATTLRSKAIEFLEKWNEKFGFH---YKELRLGFDYLKNTKKVDFPDL 152 (661)
T ss_pred HHHHHHhhcCCCCCCCCCChHHHHHHHHHHHHHHHHHHHHHhHH---HHHHHHHHHHHhccccccCcch
Confidence 44555544422222 1 1 268999999999999999864 8888889999987 67889864
No 22
>smart00582 RPR domain present in proteins, which are involved in regulation of nuclear pre-mRNA.
Probab=95.98 E-value=0.022 Score=50.00 Aligned_cols=91 Identities=20% Similarity=0.231 Sum_probs=63.0
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhc---cCCCh
Q 011515 20 AMNIEICDMLNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIAR---KKPDT 96 (484)
Q Consensus 20 ~~ileICD~In~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~---~k~d~ 96 (484)
..|..+...+-.....+++.+..|.++++...+..-+..|-|++.+++||+...-..+ ...|...+..++. ...+.
T Consensus 14 ~~I~~lt~~~~~~~~~a~~Iv~~i~~~~~~~~~~~kL~~LYlindIl~n~~~~~~~~f-~~~~~~~~~~~~~~~~~~~~~ 92 (121)
T smart00582 14 ESIQTLTKWAIEHASHAKEIVELWEKYIKKAPPPRKLPLLYLLDSIVQNSKRKYGSEF-GDELGPVFQDALRDVLGAAND 92 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccceehhHHhHHHHHHHHhhccHHHH-HHHHHHHHHHHHHHHHHhCCH
Confidence 3444444444444446789999999999877777788899999999999976642222 1234444433332 23447
Q ss_pred hHHHHHHHHHHHHHH
Q 011515 97 HVKEKILILIDTWQE 111 (484)
Q Consensus 97 ~VkeKiLeLIq~Wa~ 111 (484)
.+|+|+..++..|.+
T Consensus 93 ~~~~ki~kll~iW~~ 107 (121)
T smart00582 93 ETKKKIRRLLNIWEE 107 (121)
T ss_pred HHHHHHHHHHHHHhc
Confidence 899999999999998
No 23
>KOG0251 consensus Clathrin assembly protein AP180 and related proteins, contain ENTH domain [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=94.30 E-value=0.11 Score=56.93 Aligned_cols=80 Identities=23% Similarity=0.263 Sum_probs=74.4
Q ss_pred hHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHhcccchhhhhhcch
Q 011515 2 VNSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRIGSR-NSKVQLLALTLLETIIKNCGDIVHMHVAEK 80 (484)
Q Consensus 2 v~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL~s~-np~vqllAL~LLE~cVKNCG~~Fh~eVask 80 (484)
++..|-|||+.....|+-..+-.|--.++..+.....++.+|-+||++. |=-|++-||.|+.-+++.+...|+.++...
T Consensus 24 l~~AV~KATsh~~~ppk~k~l~~Il~~ts~~~~~i~~~v~aLs~Rl~~TrnW~VAlKsLIliH~ll~~G~~~f~~~l~~~ 103 (491)
T KOG0251|consen 24 LEKAVVKATSHDDMPPKDKYLDEILSATSSSPASIPSCVHALSERLNKTRNWTVALKALILIHRLLKEGDPSFEQELLSR 103 (491)
T ss_pred HHHHHHhhccCCCCCccHHHHHHHHHHhcCCcccHHHHHHHHHHHhCCCcceeehHHHHHHHHHHHhcCcHHHHHHHHhc
Confidence 4678999999999999999999999999999999999999999999876 999999999999999999999999888876
Q ss_pred H
Q 011515 81 N 81 (484)
Q Consensus 81 ~ 81 (484)
.
T Consensus 104 ~ 104 (491)
T KOG0251|consen 104 N 104 (491)
T ss_pred c
Confidence 5
No 24
>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=92.21 E-value=0.48 Score=47.43 Aligned_cols=76 Identities=21% Similarity=0.165 Sum_probs=60.3
Q ss_pred hHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHhcccchhhhhhc
Q 011515 2 VNSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRIGSR-NSKVQLLALTLLETIIKNCGDIVHMHVA 78 (484)
Q Consensus 2 v~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL~s~-np~vqllAL~LLE~cVKNCG~~Fh~eVa 78 (484)
++..|-|||+....-|+-..+-.|.-.... +.....++.+|.+|+... +..|++-+|.|+.-|++-+...|-.++.
T Consensus 4 l~~av~KAT~~~~~ppk~Khv~~il~~t~~-~~~~~~~~~~l~~Rl~~~~~w~V~~K~Lil~H~llr~G~~~~~~~~~ 80 (280)
T PF07651_consen 4 LEKAVIKATSHDEAPPKEKHVREILSATSS-PESVAFLFWALSRRLPLTRNWIVALKALILLHRLLRDGHPSFLQELL 80 (280)
T ss_dssp HHHHHHHHT-SSS---HHHHHHHHHHHCST-TS-HHHHHHHHHHHCTSS-SHHHHHHHHHHHHHHHHHS-CHHHHHHH
T ss_pred HHHHHHHHcCCCCCCCCHHHHHHHHHHhcC-CccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHcCchHHHHHHH
Confidence 467899999998888999999888877777 788999999999999875 9999999999999999988666655444
No 25
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=90.90 E-value=3.4 Score=33.23 Aligned_cols=86 Identities=14% Similarity=0.222 Sum_probs=65.2
Q ss_pred HHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHH
Q 011515 3 NSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNV 82 (484)
Q Consensus 3 ~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~F 82 (484)
+.+++...+ ++||..-...|..+..- +..+++..|.+.+++.++.+...|+.-|..+ ++++.
T Consensus 2 ~~L~~~l~~----~~~~~vr~~a~~~L~~~--~~~~~~~~L~~~l~d~~~~vr~~a~~aL~~i------------~~~~~ 63 (88)
T PF13646_consen 2 PALLQLLQN----DPDPQVRAEAARALGEL--GDPEAIPALIELLKDEDPMVRRAAARALGRI------------GDPEA 63 (88)
T ss_dssp HHHHHHHHT----SSSHHHHHHHHHHHHCC--THHHHHHHHHHHHTSSSHHHHHHHHHHHHCC------------HHHHT
T ss_pred HHHHHHHhc----CCCHHHHHHHHHHHHHc--CCHhHHHHHHHHHcCCCHHHHHHHHHHHHHh------------CCHHH
Confidence 455555533 36888888888888843 4679999999999999999999999888743 46778
Q ss_pred HHHHHHHhccCCChhHHHHHHHHH
Q 011515 83 LHEMVKIARKKPDTHVKEKILILI 106 (484)
Q Consensus 83 LneLvkLv~~k~d~~VkeKiLeLI 106 (484)
+..|.+++....+..||..+..-|
T Consensus 64 ~~~L~~~l~~~~~~~vr~~a~~aL 87 (88)
T PF13646_consen 64 IPALIKLLQDDDDEVVREAAAEAL 87 (88)
T ss_dssp HHHHHHHHTC-SSHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCcHHHHHHHHhhc
Confidence 888999887766677787766543
No 26
>KOG2057 consensus Predicted equilibrative nucleoside transporter protein [Nucleotide transport and metabolism]
Probab=90.38 E-value=1.4 Score=45.91 Aligned_cols=102 Identities=16% Similarity=0.151 Sum_probs=66.8
Q ss_pred HHHHHcCCCCCCcCHHHHHHHHHHHhC-CCCCHHHHHHHHHHHhCC---CCHHHHHHHHHHHHHHHhcccchhhhhhcch
Q 011515 5 MVDRATSDMLIGPDWAMNIEICDMLNH-DPGQAKDVVKGIKKRIGS---RNSKVQLLALTLLETIIKNCGDIVHMHVAEK 80 (484)
Q Consensus 5 lIekATse~l~~~Dw~~ileICD~In~-~~~~akeAvraIrKRL~s---~np~vqllAL~LLE~cVKNCG~~Fh~eVask 80 (484)
-|..||++.--+|-=.++-+||+.-.. --+.--+.+..|-.|+-. .+=+.++-+|.||+.|+||+.++|-.+..
T Consensus 27 ~VREATNdDPWGPsG~lMgeIaeaTfmry~EdFpelmnmL~qRMLedNK~~WRRVYKSLiLLaYLikNGSER~VqeAR-- 104 (499)
T KOG2057|consen 27 DVREATNDDPWGPSGPLMGEIAEATFMRYMEDFPELMNMLFQRMLEDNKDAWRRVYKSLILLAYLIKNGSERFVQEAR-- 104 (499)
T ss_pred HHHhhccCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcccHHHHHHHH--
Confidence 455666664444444567788877554 223345666666667632 34567889999999999999999987653
Q ss_pred HHHHHHHHHhccC--------CChhHHHHHHHHHHH
Q 011515 81 NVLHEMVKIARKK--------PDTHVKEKILILIDT 108 (484)
Q Consensus 81 ~FLneLvkLv~~k--------~d~~VkeKiLeLIq~ 108 (484)
+-.=+|++|-+-+ --..+|.|+.++|.-
T Consensus 105 Eh~YdLR~LEnYhfiDEhGKDQGINIR~kVKeilEf 140 (499)
T KOG2057|consen 105 EHAYDLRRLENYHFIDEHGKDQGINIRHKVKEILEF 140 (499)
T ss_pred HHHHHHHhhhhccchhhhCccccccHHHHHHHHHHH
Confidence 4455666654332 124789999888753
No 27
>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=89.35 E-value=3.9 Score=39.24 Aligned_cols=79 Identities=18% Similarity=0.247 Sum_probs=52.6
Q ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhccc---chhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHHHHH
Q 011515 36 AKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCG---DIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTWQEA 112 (484)
Q Consensus 36 akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG---~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~a 112 (484)
++-....|..-++++|+.+-..++..|..++.++| ..+.....-+.++..|.+.+.. .+.+||+-..+++..+...
T Consensus 129 ~~~~~~~l~~~~~~Kn~~vR~~~~~~l~~~l~~~~~~~~~l~~~~~~~~l~~~l~~~l~D-~~~~VR~~Ar~~~~~l~~~ 207 (228)
T PF12348_consen 129 PKILLEILSQGLKSKNPQVREECAEWLAIILEKWGSDSSVLQKSAFLKQLVKALVKLLSD-ADPEVREAARECLWALYSH 207 (228)
T ss_dssp -HHHHHHHHHHTT-S-HHHHHHHHHHHHHHHTT-----GGG--HHHHHHHHHHHHHHHTS-S-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHccchHhhhcccchHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHH
Confidence 34448888888999999999999999999999999 3333222123444445555554 5789999999999999888
Q ss_pred hCC
Q 011515 113 FGG 115 (484)
Q Consensus 113 F~~ 115 (484)
|+.
T Consensus 208 ~~~ 210 (228)
T PF12348_consen 208 FPE 210 (228)
T ss_dssp H-H
T ss_pred CCH
Confidence 863
No 28
>KOG2160 consensus Armadillo/beta-catenin-like repeat-containing protein [Posttranslational modification, protein turnover, chaperones]
Probab=88.48 E-value=1.5 Score=46.15 Aligned_cols=92 Identities=16% Similarity=0.196 Sum_probs=70.1
Q ss_pred HHHHHHHHHhCCCC--CHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhH
Q 011515 21 MNIEICDMLNHDPG--QAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHV 98 (484)
Q Consensus 21 ~ileICD~In~~~~--~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~V 98 (484)
-++++|+-|..--+ .-.-...++. -|++.+..+-.+|..++-+|+.|- .+.+.+|-...|+..|.++++...+.+|
T Consensus 106 ~Le~lve~iDnAndl~~~ggl~~ll~-~l~~~~~~lR~~Aa~Vigt~~qNN-P~~Qe~v~E~~~L~~Ll~~ls~~~~~~~ 183 (342)
T KOG2160|consen 106 NLEELVEDIDNANDLISLGGLVPLLG-YLENSDAELRELAARVIGTAVQNN-PKSQEQVIELGALSKLLKILSSDDPNTV 183 (342)
T ss_pred HHHHHHHhhhhHHhHhhccCHHHHHH-HhcCCcHHHHHHHHHHHHHHHhcC-HHHHHHHHHcccHHHHHHHHccCCCchH
Confidence 34555555543211 1122333444 889999999999999999999998 5778889899999999999997778899
Q ss_pred HHHHHHHHHHHHHHhC
Q 011515 99 KEKILILIDTWQEAFG 114 (484)
Q Consensus 99 keKiLeLIq~Wa~aF~ 114 (484)
|.|+|.-|...=.-|+
T Consensus 184 r~kaL~AissLIRn~~ 199 (342)
T KOG2160|consen 184 RTKALFAISSLIRNNK 199 (342)
T ss_pred HHHHHHHHHHHHhcCc
Confidence 9999998888766654
No 29
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=83.01 E-value=12 Score=35.13 Aligned_cols=88 Identities=13% Similarity=0.127 Sum_probs=72.4
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHH
Q 011515 20 AMNIEICDMLNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVK 99 (484)
Q Consensus 20 ~~ileICD~In~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~Vk 99 (484)
..+.-+||++-.-+.-...-+..|.++|.++++.|-..||.+|--|+.+.--++..+ ++.++.+++.. .+++|+
T Consensus 7 n~i~~l~DL~~r~~~~ve~~~~~l~~~L~D~~~~VR~~al~~Ls~Li~~d~ik~k~~-----l~~~~l~~l~D-~~~~Ir 80 (178)
T PF12717_consen 7 NAIIALGDLCIRYPNLVEPYLPNLYKCLRDEDPLVRKTALLVLSHLILEDMIKVKGQ-----LFSRILKLLVD-ENPEIR 80 (178)
T ss_pred HHHHHHHHHHHhCcHHHHhHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCceeehhh-----hhHHHHHHHcC-CCHHHH
Confidence 356789999999887788899999999999999999999999999999976665533 34555555543 578999
Q ss_pred HHHHHHHHHHHHHh
Q 011515 100 EKILILIDTWQEAF 113 (484)
Q Consensus 100 eKiLeLIq~Wa~aF 113 (484)
.-+...+.++....
T Consensus 81 ~~A~~~~~e~~~~~ 94 (178)
T PF12717_consen 81 SLARSFFSELLKKR 94 (178)
T ss_pred HHHHHHHHHHHHhc
Confidence 99999999998863
No 30
>PF04818 CTD_bind: RNA polymerase II-binding domain.; InterPro: IPR006903 This entry represents a conserved region found in a number of uncharacterised eukaryotic proteins.; PDB: 2L0I_A 2KM4_A 3D9I_B 3D9N_B 3D9O_A 3D9P_B 3D9K_A 3D9M_A 3D9J_A 3D9L_A ....
Probab=81.65 E-value=3.5 Score=32.37 Aligned_cols=54 Identities=24% Similarity=0.304 Sum_probs=34.0
Q ss_pred HHHHHHHHHHhcccchhhhhhcchHHHHHHHHH---hccCCChhHHHHHHHHHHHHHH
Q 011515 57 LALTLLETIIKNCGDIVHMHVAEKNVLHEMVKI---ARKKPDTHVKEKILILIDTWQE 111 (484)
Q Consensus 57 lAL~LLE~cVKNCG~~Fh~eVask~FLneLvkL---v~~k~d~~VkeKiLeLIq~Wa~ 111 (484)
.-|-|++..++||...-..++. ..|-.-|..+ +....+.++++|+..+|..|.+
T Consensus 3 ~~lYl~ndI~q~sk~k~~~~f~-~~F~~~l~~~~~~~~~~~~~~~~~kv~rll~iW~~ 59 (64)
T PF04818_consen 3 ALLYLANDILQNSKRKNPDEFA-PAFSPVLPDAFAHAYKNVDPEVRKKVQRLLNIWEE 59 (64)
T ss_dssp HHHHHHHHHHHHHHHHTTHCHH-HHHHCCHHHHHHHHCCCS-HHHHHHHHHHHHHHHH
T ss_pred ceeehHHHHHHHhhhcChHHHH-HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhC
Confidence 4578899999999543111121 2333333333 3334589999999999999986
No 31
>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=79.53 E-value=33 Score=29.96 Aligned_cols=104 Identities=10% Similarity=0.047 Sum_probs=66.2
Q ss_pred hHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCH-----------HHHHHHHHHHHHHHhccc
Q 011515 2 VNSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRIGSRNS-----------KVQLLALTLLETIIKNCG 70 (484)
Q Consensus 2 v~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL~s~np-----------~vqllAL~LLE~cVKNCG 70 (484)
++++|+..|+.... .|-..+-.+.-. =..-..+.+-+..|..|.....+ .++.+.+.+|-.-|.|+.
T Consensus 10 l~~Li~~L~~~~~~-~d~~f~~~Fllt-yr~F~tp~~ll~~L~~rf~~~~~~~~~~~~~~~~~~~~rv~~~l~~Wv~~~~ 87 (127)
T smart00229 10 LEKLIEHLTEAFDK-ADPFFVETFLLT-YRSFITTQELLQLLLYRYNAIPPESWVERKVNPLRVKNRVLNILRHWVENYW 87 (127)
T ss_pred HHHHHHHHcCCCcC-CCHHHHHHHHHH-hhhhCCHHHHHHHHHHHhCCCCcHHHHHHHhhHHHHHHHHHHHHHHHHHHCC
Confidence 57899999998653 342222222111 13445678888888888875333 367788899999999998
Q ss_pred chhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHH
Q 011515 71 DIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILID 107 (484)
Q Consensus 71 ~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq 107 (484)
..|...-.-..+|.++...+.........+++.+++.
T Consensus 88 ~dF~~~~~l~~~l~~f~~~~~~~~~~~~~~~l~~~~~ 124 (127)
T smart00229 88 QDFEDDPKLILRLLEFLDLVDQEKGPGLVTSLQELLQ 124 (127)
T ss_pred cccccCHHHHHHHHHHHHHHhhCcCCCHHHHHHHHHH
Confidence 8888775455667776666544323445555555544
No 32
>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=78.87 E-value=17 Score=30.15 Aligned_cols=69 Identities=13% Similarity=0.153 Sum_probs=55.0
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHH
Q 011515 38 DVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDT 108 (484)
Q Consensus 38 eAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~ 108 (484)
+++..|.+-|.+.+++++..|+..|-.+..++... ...+....++..|++++... +..|++.++.++..
T Consensus 49 ~~i~~l~~~l~~~~~~v~~~a~~~L~~l~~~~~~~-~~~~~~~g~l~~l~~~l~~~-~~~~~~~a~~~l~~ 117 (120)
T cd00020 49 GGLPALVQLLKSEDEEVVKAALWALRNLAAGPEDN-KLIVLEAGGVPKLVNLLDSS-NEDIQKNATGALSN 117 (120)
T ss_pred CChHHHHHHHhCCCHHHHHHHHHHHHHHccCcHHH-HHHHHHCCChHHHHHHHhcC-CHHHHHHHHHHHHH
Confidence 56778888888999999999999999999988643 33344566899999988764 77899888887754
No 33
>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=77.39 E-value=14 Score=35.45 Aligned_cols=96 Identities=18% Similarity=0.272 Sum_probs=62.3
Q ss_pred CCcCHHHHH----HHHHHHhCC--CCCHHHH---HH----HHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchH
Q 011515 15 IGPDWAMNI----EICDMLNHD--PGQAKDV---VK----GIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKN 81 (484)
Q Consensus 15 ~~~Dw~~il----eICD~In~~--~~~akeA---vr----aIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~ 81 (484)
.+.||..-. .+-.+++.. .....+. ++ .|.+.+.+.+..++..|+.+|..|...+|..|...+ ..
T Consensus 17 ~~~~W~~r~~al~~L~~l~~~~~~~~~~~~~~~~l~~~~~~i~~~l~d~Rs~v~~~A~~~l~~l~~~l~~~~~~~~--~~ 94 (228)
T PF12348_consen 17 SESDWEERVEALQKLRSLIKGNAPEDFPPDFVECLRQLLDAIIKQLSDLRSKVSKTACQLLSDLARQLGSHFEPYA--DI 94 (228)
T ss_dssp T-SSHHHHHHHHHHHHHHHHH-B-----HHHHHHHH---HHHHH-S-HH---HHHHHHHHHHHHHHHHGGGGHHHH--HH
T ss_pred CccCHHHHHHHHHHHHHHHHcCCccccHHHHHHHHHHhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhHhHHHHH--HH
Confidence 567998644 444555555 3333333 33 555788888999999999999999999999987653 56
Q ss_pred HHHHHHHHhccCCChhHHHHHHHHHHHHHHHh
Q 011515 82 VLHEMVKIARKKPDTHVKEKILILIDTWQEAF 113 (484)
Q Consensus 82 FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~aF 113 (484)
|+..|.+.+..+ ..-|++.+...|..+....
T Consensus 95 ~l~~Ll~~~~~~-~~~i~~~a~~~L~~i~~~~ 125 (228)
T PF12348_consen 95 LLPPLLKKLGDS-KKFIREAANNALDAIIESC 125 (228)
T ss_dssp HHHHHHHGGG----HHHHHHHHHHHHHHHTTS
T ss_pred HHHHHHHHHccc-cHHHHHHHHHHHHHHHHHC
Confidence 888888877653 3579999999998888754
No 34
>PF12210 Hrs_helical: Hepatocyte growth factor-regulated tyrosine kinase substrate; InterPro: IPR024641 This domain comprises the helical region of hepatocyte growth factor-regulated tyrosine kinase substrate (HRS). It is approximately 100 amino acids in length. Hrs, together with signal transducing adaptor molecule (STAM), forms the ESCRT-0 complex, which sorts ubiquitinated cell surface receptors to lysosomes for degradation []. ; PDB: 3F1I_H.
Probab=74.83 E-value=7 Score=33.97 Aligned_cols=55 Identities=4% Similarity=0.200 Sum_probs=40.6
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCCccCchHHHHHHHHHHHHHHHHHHHHhhccCCH
Q 011515 189 IQNARGIMDVLAEMLNALDPNNKEGLRQEVIVDLVDQCRTYKQRVVHLVNSTADE 243 (484)
Q Consensus 189 Le~ak~nv~LL~EML~~~~P~~~e~~d~Eli~EL~~~Cr~~q~rV~rLI~~~~DE 243 (484)
+...+..+++|.+=+......+.+...+..++.||.+.-.|.++|+++|++.++.
T Consensus 4 ~~~l~~~v~if~nRmksns~RGrsIanDsaVqsLF~~lt~mH~~LL~~i~~~ee~ 58 (96)
T PF12210_consen 4 CNTLRSSVEIFVNRMKSNSSRGRSIANDSAVQSLFQTLTAMHPQLLKYIQEQEEK 58 (96)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTT--GGG-HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhHhcCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566778888877554443445677788899999999999999999999886543
No 35
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=74.44 E-value=17 Score=29.10 Aligned_cols=57 Identities=9% Similarity=0.222 Sum_probs=45.4
Q ss_pred HHHHHHHh-CCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHH
Q 011515 40 VKGIKKRI-GSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTW 109 (484)
Q Consensus 40 vraIrKRL-~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~W 109 (484)
+..|.+.| +++++.+...|+.+|. ++.+.+.+..|.++++. .+..||..+...|..-
T Consensus 1 i~~L~~~l~~~~~~~vr~~a~~~L~------------~~~~~~~~~~L~~~l~d-~~~~vr~~a~~aL~~i 58 (88)
T PF13646_consen 1 IPALLQLLQNDPDPQVRAEAARALG------------ELGDPEAIPALIELLKD-EDPMVRRAAARALGRI 58 (88)
T ss_dssp HHHHHHHHHTSSSHHHHHHHHHHHH------------CCTHHHHHHHHHHHHTS-SSHHHHHHHHHHHHCC
T ss_pred CHHHHHHHhcCCCHHHHHHHHHHHH------------HcCCHhHHHHHHHHHcC-CCHHHHHHHHHHHHHh
Confidence 35677888 8999999999998887 44566889999998854 6789999888777644
No 36
>PF08167 RIX1: rRNA processing/ribosome biogenesis
Probab=71.05 E-value=38 Score=31.66 Aligned_cols=75 Identities=19% Similarity=0.292 Sum_probs=54.6
Q ss_pred HHHHHHHHHHHh----CCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHHHH
Q 011515 36 AKDVVKGIKKRI----GSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTWQE 111 (484)
Q Consensus 36 akeAvraIrKRL----~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~ 111 (484)
.+.++..++.|| +++++..-..++.|+...+.+||...-.+-+ ..|+..|.+++.+..+..+++-++..+..--.
T Consensus 19 ~~~~l~~l~~ri~~LL~s~~~~~rw~G~~Ll~~~~~~~~~e~l~~~~-~~W~~~Ll~~L~~~~~~~~~~~ai~~L~~l~~ 97 (165)
T PF08167_consen 19 SKSALHKLVTRINSLLQSKSAYSRWAGLCLLKVTVEQCSWEILLSHG-SQWLRALLSILEKPDPPSVLEAAIITLTRLFD 97 (165)
T ss_pred CHHHHHHHHHHHHHHhCCCChhhHHHHHHHHHHHHHHhhHHHHHHHH-HHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHH
Confidence 355666666555 6788999999999999999999654443333 57999999999886666777766655554443
No 37
>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=69.39 E-value=71 Score=27.34 Aligned_cols=85 Identities=13% Similarity=0.173 Sum_probs=57.0
Q ss_pred hHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCC--------------CHHHHHHHHHHHHHHHh
Q 011515 2 VNSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRIGSR--------------NSKVQLLALTLLETIIK 67 (484)
Q Consensus 2 v~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL~s~--------------np~vqllAL~LLE~cVK 67 (484)
+++||+++|++.. ..|-..+-.+.-. =..-..+.+.+..|..|.... ...++++.+.+|-.-|.
T Consensus 2 l~~Li~~L~~~~~-~~d~~f~~~FllT-yrsF~s~~~ll~~L~~rf~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~Wv~ 79 (122)
T cd06224 2 LEALIEHLTSTFD-MPDPSFVSTFLLT-YRSFTTPTELLEKLIERYEIAPPENLEYNDWDKKKSKPIRLRVLNVLRTWVE 79 (122)
T ss_pred HHHHHHHHcCCCc-cccHHHHHHHHHH-hhhhCCHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5789999999977 2233322222111 133456788888888888643 24467888999999999
Q ss_pred cccchhhhhhcchHHHHHHHHHhc
Q 011515 68 NCGDIVHMHVAEKNVLHEMVKIAR 91 (484)
Q Consensus 68 NCG~~Fh~eVask~FLneLvkLv~ 91 (484)
+|...|+ .+..++..|...+.
T Consensus 80 ~~~~df~---~d~~l~~~l~~F~~ 100 (122)
T cd06224 80 NYPYDFF---DDEELLELLEEFLN 100 (122)
T ss_pred hCCCccc---ccHHHHHHHHHHHH
Confidence 9999986 45566666666554
No 38
>PF11841 DUF3361: Domain of unknown function (DUF3361)
Probab=65.13 E-value=24 Score=33.42 Aligned_cols=60 Identities=15% Similarity=0.262 Sum_probs=49.3
Q ss_pred CCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHHHH
Q 011515 50 RNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTWQE 111 (484)
Q Consensus 50 ~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~ 111 (484)
.++.+..+||.+||.+|.|.. ..+..|..+==+..|++.+.. ++.+++...+.||-..-.
T Consensus 72 ~d~~i~q~sLaILEs~Vl~S~-~ly~~V~~evt~~~Li~hLq~-~~~~iq~naiaLinAL~~ 131 (160)
T PF11841_consen 72 MDASILQRSLAILESIVLNSP-KLYQLVEQEVTLESLIRHLQV-SNQEIQTNAIALINALFL 131 (160)
T ss_pred ccchHHHHHHHHHHHHHhCCH-HHHHHHhccCCHHHHHHHHHc-CCHHHHHHHHHHHHHHHh
Confidence 379999999999999999874 556678877667888888877 688999999999876543
No 39
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=64.42 E-value=10 Score=42.46 Aligned_cols=78 Identities=23% Similarity=0.371 Sum_probs=61.0
Q ss_pred CCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHHH
Q 011515 31 HDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTWQ 110 (484)
Q Consensus 31 ~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa 110 (484)
...-.++..|-+|-++|...-+..-|.++.+||..+||-|...-..+ ++.........+. +++...|.++..++.+|.
T Consensus 33 En~~~a~~iv~~iE~hi~kcpp~~kL~~~y~~dsi~knvg~py~~~f-s~~l~a~f~~~~~-~vd~r~r~~l~~~~~tw~ 110 (579)
T KOG2071|consen 33 ENLPFAKSIVSAIEAHIAKCPPSQKLPVMYLLDSIVKNVGSPYTTAF-SRNLVATFICAFT-KVDERTRTSLFKLRATWD 110 (579)
T ss_pred hcccccHHHHHHHHHHHhhCCcccccchhhhhHHHHhhcCCcchhhh-hhhHHHHHHHHHh-hccccccchhHhhHHhhc
Confidence 34445899999999999999999999999999999999999854333 3443333333222 368899999999999999
No 40
>PF06812 ImpA-rel_N: ImpA-related N-terminal; InterPro: IPR010657 This entry represents a conserved region located towards the N-terminal end of ImpA and related proteins. ImpA is an inner membrane protein, which has been suggested to be involved with proteins that are exported and associated with colony variations in Actinobacillus actinomycetemcomitans []. Note that many members are hypothetical proteins.
Probab=62.91 E-value=32 Score=27.01 Aligned_cols=58 Identities=19% Similarity=0.139 Sum_probs=49.0
Q ss_pred CHHHHHHHHHHHh-CCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhh
Q 011515 18 DWAMNIEICDMLN-HDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHM 75 (484)
Q Consensus 18 Dw~~ileICD~In-~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~ 75 (484)
||..+.+.|..+- +..-.-+-|+-.+.-+++.....--..+|.+|..|+.+.....|-
T Consensus 1 DW~~v~~~~~~lL~~~sKDlrv~~~l~~a~~~~~g~~gl~~gl~ll~~ll~~~W~~l~P 59 (62)
T PF06812_consen 1 DWDKVEELALELLSEQSKDLRVAVWLTEALLRLEGLAGLAEGLELLADLLENYWDSLHP 59 (62)
T ss_pred CHHHHHHHHHHHHHHcCchHHHHHHHHHHHHHccChhHHHHHHHHHHHHHHHCCcccCC
Confidence 8999999997766 555567888888999998888888889999999999998887764
No 41
>KOG1077 consensus Vesicle coat complex AP-2, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=61.97 E-value=27 Score=40.26 Aligned_cols=72 Identities=29% Similarity=0.341 Sum_probs=56.6
Q ss_pred HHHHHHHhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhcc-CCChhHHHH
Q 011515 23 IEICDMLNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARK-KPDTHVKEK 101 (484)
Q Consensus 23 leICD~In~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~-k~d~~VkeK 101 (484)
|-|.=++|.+.+--|.++..||+-|.++|+..+.+||. ||-|-|.+ +++ ..|-+++-||+-. ....-||+|
T Consensus 96 l~is~L~n~n~dl~klvin~iknDL~srn~~fv~LAL~----~I~niG~r---e~~-ea~~~DI~KlLvS~~~~~~vkqk 167 (938)
T KOG1077|consen 96 LFISLLLNENSDLMKLVINSIKNDLSSRNPTFVCLALH----CIANIGSR---EMA-EAFADDIPKLLVSGSSMDYVKQK 167 (938)
T ss_pred HHHHHHHhcchHHHHHHHHHHHhhhhcCCcHHHHHHHH----HHHhhccH---hHH-HHhhhhhHHHHhCCcchHHHHHH
Confidence 44677788888889999999999999999999999996 78898865 444 4677888887644 344567776
Q ss_pred H
Q 011515 102 I 102 (484)
Q Consensus 102 i 102 (484)
.
T Consensus 168 a 168 (938)
T KOG1077|consen 168 A 168 (938)
T ss_pred H
Confidence 4
No 42
>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=60.32 E-value=33 Score=28.31 Aligned_cols=72 Identities=18% Similarity=0.163 Sum_probs=56.8
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHHHHH
Q 011515 39 VVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTWQEA 112 (484)
Q Consensus 39 AvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~a 112 (484)
.+..|.+-|++.+..+...|+..|..+.++... ....+.+.+++..|.+++.. .+..|+..++..+..+...
T Consensus 8 ~i~~l~~~l~~~~~~~~~~a~~~l~~l~~~~~~-~~~~~~~~~~i~~l~~~l~~-~~~~v~~~a~~~L~~l~~~ 79 (120)
T cd00020 8 GLPALVSLLSSSDENVQREAAWALSNLSAGNND-NIQAVVEAGGLPALVQLLKS-EDEEVVKAALWALRNLAAG 79 (120)
T ss_pred ChHHHHHHHHcCCHHHHHHHHHHHHHHhcCCHH-HHHHHHHCCChHHHHHHHhC-CCHHHHHHHHHHHHHHccC
Confidence 567788888888999999999999999987533 33344556889999998876 4789999999988888653
No 43
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=59.87 E-value=34 Score=33.56 Aligned_cols=101 Identities=16% Similarity=0.159 Sum_probs=58.3
Q ss_pred CcCHHHHHHHHHH-HhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhc-----chHHHHHHHHH
Q 011515 16 GPDWAMNIEICDM-LNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVA-----EKNVLHEMVKI 89 (484)
Q Consensus 16 ~~Dw~~ileICD~-In~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVa-----sk~FLneLvkL 89 (484)
..+|=.-+.+|=+ .|++..++-.|.+.|.+.+-+.+. .=|.-..++||++|+..=+ .++++..+..+
T Consensus 36 ~e~lf~ELsFCILTANsSA~~~~~~q~~lG~gfly~~~-------eEL~e~Lk~~g~Rf~n~raeyIVeaR~~~~~lk~~ 108 (210)
T COG1059 36 KEDLFKELSFCILTANSSATMGLRAQNELGDGFLYLSE-------EELREKLKEVGYRFYNVRAEYIVEAREKFDDLKII 108 (210)
T ss_pred HHHHHHHHHHHhccccchHHHHHHHHHHhccccccCCH-------HHHHHHHHHhcchhcccchHHHHHHHHHHHHHHHH
Confidence 3456555566644 445555555666666655555433 4456667899999997544 45666677777
Q ss_pred hccCCChhH-HHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHhcC
Q 011515 90 ARKKPDTHV-KEKILILIDTWQEAFGGPRARYPQYYAAYQELLRAGA 135 (484)
Q Consensus 90 v~~k~d~~V-keKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~kGi 135 (484)
++...+..| |+.+++-|. + =.+.+|=+.|+.-|+
T Consensus 109 v~~~~~~~vaRE~Lv~nik-------G-----iGyKEASHFLRNVG~ 143 (210)
T COG1059 109 VKADENEKVARELLVENIK-------G-----IGYKEASHFLRNVGF 143 (210)
T ss_pred HhcCcchHHHHHHHHHHcc-------c-----ccHHHHHHHHHhcCh
Confidence 775445554 333333222 1 124566677777665
No 44
>PRK09687 putative lyase; Provisional
Probab=55.31 E-value=1.1e+02 Score=31.08 Aligned_cols=72 Identities=15% Similarity=0.163 Sum_probs=43.5
Q ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHHH---------HHHh---cccchhh-----hhhcchHHHHHHHHHhccCCChhH
Q 011515 36 AKDVVKGIKKRIGSRNSKVQLLALTLLE---------TIIK---NCGDIVH-----MHVAEKNVLHEMVKIARKKPDTHV 98 (484)
Q Consensus 36 akeAvraIrKRL~s~np~vqllAL~LLE---------~cVK---NCG~~Fh-----~eVask~FLneLvkLv~~k~d~~V 98 (484)
..+++..|.+.|...+..|...|+.-|. .+++ +...++. -++++++++..|.+++....|..|
T Consensus 190 ~~~~~~~L~~~L~D~~~~VR~~A~~aLg~~~~~~av~~Li~~L~~~~~~~~a~~ALg~ig~~~a~p~L~~l~~~~~d~~v 269 (280)
T PRK09687 190 NPDIREAFVAMLQDKNEEIRIEAIIGLALRKDKRVLSVLIKELKKGTVGDLIIEAAGELGDKTLLPVLDTLLYKFDDNEI 269 (280)
T ss_pred CHHHHHHHHHHhcCCChHHHHHHHHHHHccCChhHHHHHHHHHcCCchHHHHHHHHHhcCCHhHHHHHHHHHhhCCChhH
Confidence 4566777777777777777766654443 2222 2111111 345567777777777776567777
Q ss_pred HHHHHHHHH
Q 011515 99 KEKILILID 107 (484)
Q Consensus 99 keKiLeLIq 107 (484)
+.++++-+.
T Consensus 270 ~~~a~~a~~ 278 (280)
T PRK09687 270 ITKAIDKLK 278 (280)
T ss_pred HHHHHHHHh
Confidence 777776654
No 45
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members
Probab=52.63 E-value=35 Score=28.71 Aligned_cols=42 Identities=14% Similarity=0.245 Sum_probs=29.0
Q ss_pred hccCCChhHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHhc
Q 011515 90 ARKKPDTHVKEKILILIDTWQEAFGGPRARYPQYYAAYQELLRAG 134 (484)
Q Consensus 90 v~~k~d~~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~kG 134 (484)
++...+..+++++..|++.|.+..+++. ..+..+.+.|++-|
T Consensus 33 Ie~~~~~dl~eq~~~mL~~W~~~~~~~~---atv~~L~~AL~~~g 74 (86)
T cd08779 33 IKYNNRDDLDEQIFDMLFSWAQRQAGDP---DAVGKLVTALEESG 74 (86)
T ss_pred HHHHCccCHHHHHHHHHHHHHHhcCCCc---hHHHHHHHHHHHcC
Confidence 4433345799999999999999876532 23556666676644
No 46
>KOG1293 consensus Proteins containing armadillo/beta-catenin-like repeat [General function prediction only]
Probab=51.91 E-value=51 Score=37.64 Aligned_cols=74 Identities=14% Similarity=0.221 Sum_probs=63.5
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHHHHH
Q 011515 38 DVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTWQEA 112 (484)
Q Consensus 38 eAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~a 112 (484)
..+..|-+-+....+++--.++-+|.-+|-||...|..+.-++=|.+-+..++.. ++..|++.++.++....-.
T Consensus 461 ngId~l~s~~~~~~~n~r~~~~~~Lr~l~f~~de~~k~~~~~ki~a~~i~~l~nd-~d~~Vqeq~fqllRNl~c~ 534 (678)
T KOG1293|consen 461 NGIDILESMLTDPDFNSRANSLWVLRHLMFNCDEEEKFQLLAKIPANLILDLIND-PDWAVQEQCFQLLRNLTCN 534 (678)
T ss_pred CcHHHHHHHhcCCCchHHHHHHHHHHHHHhcchHHHHHHHHHHhhHHHHHHHHhC-CCHHHHHHHHHHHHHhhcC
Confidence 3566777788889999999999999999999999999988877777777777766 6899999999999998754
No 47
>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=51.07 E-value=1.1e+02 Score=32.93 Aligned_cols=76 Identities=21% Similarity=0.311 Sum_probs=42.1
Q ss_pred HHHhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHH
Q 011515 27 DMLNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILI 106 (484)
Q Consensus 27 D~In~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLI 106 (484)
-+...+++...-++..|+|-|.++|+.++.+||..|-.+. ..+++ ..++..+.+++.. .++.||++++..+
T Consensus 68 ~~~~~~~~~~~l~~n~l~kdl~~~n~~~~~lAL~~l~~i~-------~~~~~-~~l~~~v~~ll~~-~~~~VRk~A~~~l 138 (526)
T PF01602_consen 68 LYLHEDPELLILIINSLQKDLNSPNPYIRGLALRTLSNIR-------TPEMA-EPLIPDVIKLLSD-PSPYVRKKAALAL 138 (526)
T ss_dssp HHTTTSHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHH--------SHHHH-HHHHHHHHHHHHS-SSHHHHHHHHHHH
T ss_pred HHhhcchhHHHHHHHHHHHhhcCCCHHHHHHHHhhhhhhc-------ccchh-hHHHHHHHHHhcC-CchHHHHHHHHHH
Confidence 3344445556678888888888888888888887665433 11222 2334444444443 2345555555444
Q ss_pred HHHHH
Q 011515 107 DTWQE 111 (484)
Q Consensus 107 q~Wa~ 111 (484)
..-..
T Consensus 139 ~~i~~ 143 (526)
T PF01602_consen 139 LKIYR 143 (526)
T ss_dssp HHHHH
T ss_pred HHHhc
Confidence 44433
No 48
>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere).
Probab=50.71 E-value=81 Score=25.84 Aligned_cols=24 Identities=21% Similarity=0.486 Sum_probs=20.2
Q ss_pred hccCCChhHHHHHHHHHHHHHHHh
Q 011515 90 ARKKPDTHVKEKILILIDTWQEAF 113 (484)
Q Consensus 90 v~~k~d~~VkeKiLeLIq~Wa~aF 113 (484)
++++.+++|+..+.+||..|...+
T Consensus 50 Lrkh~~~~I~~~A~~Li~~WK~~v 73 (75)
T smart00509 50 LRKHKNEEIRKLAKKLIKSWKKLV 73 (75)
T ss_pred HHcCCcHHHHHHHHHHHHHHHHHh
Confidence 344568999999999999999876
No 49
>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=49.73 E-value=43 Score=36.02 Aligned_cols=88 Identities=20% Similarity=0.404 Sum_probs=59.7
Q ss_pred HHHHHHHHHHHhCCCCCHHH-HHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhccCCChh
Q 011515 19 WAMNIEICDMLNHDPGQAKD-VVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTH 97 (484)
Q Consensus 19 w~~ileICD~In~~~~~ake-AvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~ 97 (484)
...++.++.+.+.+++.... .+..|.+-|..+++.|+..|+.++..| .|.......+. ..+...|.+++ ..+++-
T Consensus 132 k~A~~~l~~i~~~~p~~~~~~~~~~l~~lL~d~~~~V~~~a~~~l~~i--~~~~~~~~~~~-~~~~~~L~~~l-~~~~~~ 207 (526)
T PF01602_consen 132 KKAALALLKIYRKDPDLVEDELIPKLKQLLSDKDPSVVSAALSLLSEI--KCNDDSYKSLI-PKLIRILCQLL-SDPDPW 207 (526)
T ss_dssp HHHHHHHHHHHHHCHCCHHGGHHHHHHHHTTHSSHHHHHHHHHHHHHH--HCTHHHHTTHH-HHHHHHHHHHH-TCCSHH
T ss_pred HHHHHHHHHHhccCHHHHHHHHHHHHhhhccCCcchhHHHHHHHHHHH--ccCcchhhhhH-HHHHHHhhhcc-cccchH
Confidence 45688899999999988777 599999999999999999999999999 22222211111 23333344433 235566
Q ss_pred HHHHHHHHHHHHH
Q 011515 98 VKEKILILIDTWQ 110 (484)
Q Consensus 98 VkeKiLeLIq~Wa 110 (484)
++.+++.++..+.
T Consensus 208 ~q~~il~~l~~~~ 220 (526)
T PF01602_consen 208 LQIKILRLLRRYA 220 (526)
T ss_dssp HHHHHHHHHTTST
T ss_pred HHHHHHHHHHhcc
Confidence 7777777766543
No 50
>cd00183 TFIIS_I N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme
Probab=48.43 E-value=49 Score=27.07 Aligned_cols=25 Identities=20% Similarity=0.476 Sum_probs=20.5
Q ss_pred HhccCCChhHHHHHHHHHHHHHHHh
Q 011515 89 IARKKPDTHVKEKILILIDTWQEAF 113 (484)
Q Consensus 89 Lv~~k~d~~VkeKiLeLIq~Wa~aF 113 (484)
-++++.+++|+..+.+|+..|...+
T Consensus 51 ~Lrkh~~~~i~~~A~~Lv~~Wk~~v 75 (76)
T cd00183 51 SLRKHSNEKIRKLAKALIKSWKKLV 75 (76)
T ss_pred HHHcCCcHHHHHHHHHHHHHHHHhc
Confidence 3455667999999999999999764
No 51
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=48.32 E-value=74 Score=33.11 Aligned_cols=75 Identities=19% Similarity=0.243 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHhCC
Q 011515 36 AKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTWQEAFGG 115 (484)
Q Consensus 36 akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~aF~~ 115 (484)
+.-+++.|.+-.+++|....+-.|.-|+.+.. ..+....++ .--.+..+++..++.+|+.++..||..|...+-.
T Consensus 6 ~~r~ak~l~~~~~~~n~~~~ld~l~~L~~~pv----t~ell~~Tr-~g~~vn~~~Kk~~n~ev~~~ak~Lik~Wkk~~~~ 80 (296)
T KOG1105|consen 6 ALRAAKALEKDKQSKNVEAALDLLKRLKKIPV----TLELLQETR-TGMGVNEVLKKHKNEEVRSLAKKLIKSWKKLVDK 80 (296)
T ss_pred HHHHHHHHHhhcccccHHHHHHHHHHHHhccc----HHHHHHHhh-HHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhhc
Confidence 34444554444455555555555544443322 111111111 1111122456678999999999999999998753
No 52
>PF06160 EzrA: Septation ring formation regulator, EzrA ; InterPro: IPR010379 During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation [].; GO: 0000921 septin ring assembly, 0005940 septin ring, 0016021 integral to membrane
Probab=47.96 E-value=4e+02 Score=29.91 Aligned_cols=79 Identities=16% Similarity=0.227 Sum_probs=52.3
Q ss_pred HHHHHHHHHHhcccchhhhhh---------cchHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHhCCCCCCchHHHHHH
Q 011515 57 LALTLLETIIKNCGDIVHMHV---------AEKNVLHEMVKIARKKPDTHVKEKILILIDTWQEAFGGPRARYPQYYAAY 127 (484)
Q Consensus 57 lAL~LLE~cVKNCG~~Fh~eV---------ask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y 127 (484)
.|+.-|+..+++-...|..-. ..++.+..+..-+.. =....++|=.++..-...|+. .+..+.+.|
T Consensus 161 ~a~~~Le~~L~~ie~~F~~f~~lt~~GD~~~A~eil~~l~~~~~~--l~~~~e~IP~l~~~l~~~~P~---ql~eL~~gy 235 (560)
T PF06160_consen 161 PAIEELEKQLENIEEEFSEFEELTENGDYLEAREILEKLKEETDE--LEEIMEDIPKLYKELQKEFPD---QLEELKEGY 235 (560)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH--HHHHHHHhHHHHHHHHHHhHH---HHHHHHHHH
Confidence 566777777777766665321 113333333322211 125667777888888888875 578899999
Q ss_pred HHHHHhcCCCCCC
Q 011515 128 QELLRAGAVFPQR 140 (484)
Q Consensus 128 ~~Lk~kGi~FP~~ 140 (484)
+.|+.+||.|+..
T Consensus 236 ~~m~~~gy~l~~~ 248 (560)
T PF06160_consen 236 REMEEEGYYLEHL 248 (560)
T ss_pred HHHHHCCCCCCCC
Confidence 9999999999853
No 53
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=47.51 E-value=52 Score=27.65 Aligned_cols=71 Identities=8% Similarity=0.119 Sum_probs=43.5
Q ss_pred HHHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHhcC
Q 011515 61 LLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTWQEAFGGPRARYPQYYAAYQELLRAGA 135 (484)
Q Consensus 61 LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~kGi 135 (484)
..+.+.+|-|..+..-.-.=.|-+.=+.-+....+..+++++.+||..|....+.. ..+..+.+.|++-|.
T Consensus 4 ~f~~i~~~lG~~Wk~laR~LGlse~~Id~i~~~~~~~~~eq~~~mL~~W~~~~g~~----At~~~L~~aL~~~~l 74 (86)
T cd08306 4 AFDVICENVGRDWRKLARKLGLSETKIESIEEAHPRNLREQVRQSLREWKKIKKKE----AKVADLIKALRDCQL 74 (86)
T ss_pred HHHHHHHHHhhhHHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHhHCcc----hHHHHHHHHHHHcCc
Confidence 45667777777666433333444443333332233469999999999999987642 345556666666553
No 54
>PF02854 MIF4G: MIF4G domain; InterPro: IPR003890 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 3", and is found in nuclear cap-binding proteins, eIF4G, and UPF2. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA. Nonsense-mediated mRNA decay (NMD) in eukaryotes involves UPF1, UPF2 and UPF3 to accelerate the decay rate of two unique classes of transcripts: (1) nonsense mRNAs that arise through errors in gene expression, and (2) naturally occurring transcripts that lack coding errors but have built-in features that target them for accelerated decay (error-free mRNAs). NMD can trigger decay during any round of translation and can target CBC-bound or eIF-4E-bound transcripts []. UPF2 contains MIF4G domains, while UPF3 contains an RNP domain []. ; GO: 0005515 protein binding, 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A 1HU3_A 3RK6_A ....
Probab=47.05 E-value=1e+02 Score=28.26 Aligned_cols=87 Identities=14% Similarity=0.190 Sum_probs=55.1
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCH----HHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHH----Hhcc
Q 011515 21 MNIEICDMLNHDPGQAKDVVKGIKKRIGSRNS----KVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVK----IARK 92 (484)
Q Consensus 21 ~ileICD~In~~~~~akeAvraIrKRL~s~np----~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvk----Lv~~ 92 (484)
.+.=||++.+..-...+.....|+.=+..... ......+.++=.++++||..+...=..+..++++.. .+..
T Consensus 106 ~~~fl~eL~~~~vv~~~~i~~~l~~ll~~~~~~~~~~~~~~~ie~~~~lL~~~G~~l~~~~~~~~~l~~~~~~~~~~~~~ 185 (209)
T PF02854_consen 106 NIRFLAELFNFGVVSEKIIFDILRELLSDGTDECQPPPDEENIECLCTLLKTCGKKLENSEESPKALDEIFERLQKYANS 185 (209)
T ss_dssp HHHHHHHHHHTTSSCHHHHHHHHHHHHHHTSHHCCHHTCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHH
T ss_pred hhhHHHhhHhhccccchhHHHHHHHHHhcccccccCCCcHhHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHh
Confidence 45568899998887777666666665555443 445566777777788999888822233445555443 3332
Q ss_pred ----CCChhHHHHHHHHHH
Q 011515 93 ----KPDTHVKEKILILID 107 (484)
Q Consensus 93 ----k~d~~VkeKiLeLIq 107 (484)
..+.++|-.+.+++.
T Consensus 186 ~~~~~~~~r~~~~l~~l~~ 204 (209)
T PF02854_consen 186 KKDPNLSSRIRFMLEDLIE 204 (209)
T ss_dssp CHSSSSSHHHHHHHHHHHH
T ss_pred hcccCCCHHHHHHHHHHHH
Confidence 345677777777664
No 55
>PF03670 UPF0184: Uncharacterised protein family (UPF0184); InterPro: IPR022788 This family of proteins has no known function.
Probab=46.83 E-value=53 Score=27.97 Aligned_cols=54 Identities=13% Similarity=0.231 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCCCccCchHHHHHHHHHHHHHHHHHHHHhhccC
Q 011515 186 LTEIQNARGIMDVLAEMLNALDPNNKEGLRQEVIVDLVDQCRTYKQRVVHLVNSTA 241 (484)
Q Consensus 186 lseLe~ak~nv~LL~EML~~~~P~~~e~~d~Eli~EL~~~Cr~~q~rV~rLI~~~~ 241 (484)
..|++.+...+.-|+-.|+++... .+.=...+++|.+.+|+.|..+........
T Consensus 25 ~~E~~~ins~LD~Lns~LD~LE~r--nD~l~~~L~~LLesnrq~R~e~~~~~~~~~ 78 (83)
T PF03670_consen 25 EEEYAAINSMLDQLNSCLDHLEQR--NDHLHAQLQELLESNRQIRLEFQEQLSKAP 78 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh--hhHHHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence 578889999999999999998432 222245678999999999999988776543
No 56
>PF06798 PrkA: PrkA serine protein kinase C-terminal domain; InterPro: IPR010650 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This entry is found at the C terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length. PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.
Probab=46.47 E-value=16 Score=37.01 Aligned_cols=77 Identities=16% Similarity=0.208 Sum_probs=56.0
Q ss_pred CHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccc--hhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHH-HHHH
Q 011515 35 QAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGD--IVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILID-TWQE 111 (484)
Q Consensus 35 ~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~--~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq-~Wa~ 111 (484)
.+++++++|-.-+..-.....+.++.||+.|...|.. .|..+. .++|++.|. .+...++..|++-|.+-+. .+.+
T Consensus 38 S~R~~~~~ls~a~~~~~~~~~i~p~~vl~~L~~~l~~~~~i~~e~-~~~y~~~l~-~v~~~Y~~~v~~EV~~A~~~~~ee 115 (254)
T PF06798_consen 38 SPRFVIKILSNALSSDSEEDCINPLDVLNELEEGLKDHPSISEEE-RERYLEFLK-SVRKEYDERVEKEVQEAFYYSYEE 115 (254)
T ss_pred CHhHHHHHHHHHHHhCcccceecHHHHHHHHHHHhhcccccCHHH-HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHccHH
Confidence 4899999999998886777888999999999999977 455555 466777555 6666666666666655554 4554
Q ss_pred Hh
Q 011515 112 AF 113 (484)
Q Consensus 112 aF 113 (484)
..
T Consensus 116 ~~ 117 (254)
T PF06798_consen 116 QI 117 (254)
T ss_pred HH
Confidence 43
No 57
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=45.59 E-value=52 Score=27.75 Aligned_cols=70 Identities=13% Similarity=0.209 Sum_probs=42.7
Q ss_pred HHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHhcC
Q 011515 62 LETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTWQEAFGGPRARYPQYYAAYQELLRAGA 135 (484)
Q Consensus 62 LE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~kGi 135 (484)
|..+..|-|.......-.=.|-+.=+..++...+..+.++|.+++..|.+..+. -.-+..+.+.|++-|+
T Consensus 5 L~~la~~LG~~W~~Lar~Lgls~~~I~~i~~~~p~~l~eQv~~mL~~W~~r~G~----~ATv~~L~~aL~~~~~ 74 (83)
T cd08319 5 LNQLAQRLGPEWEQVLLDLGLSQTDIYRCKENHPHNVQSQIVEALVKWRQRFGK----KATVQSLIQSLKAVEV 74 (83)
T ss_pred HHHHHHHHhhhHHHHHHHcCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHHhcCC----CCcHHHHHHHHHHcCC
Confidence 445566666655432222223333223343333447999999999999998864 2346677788887774
No 58
>PF11707 Npa1: Ribosome 60S biogenesis N-terminal; InterPro: IPR021714 Npa1p is required for ribosome biogenesis and operates in the same functional environment as Rsa3p and Dbp6p during early maturation of 60S ribosomal subunits []. The protein partners of Npa1p include eight putative helicases as well as the novel Npa2p factor. Npa1p can also associate with a subset of H/ACA and C/D small nucleolar RNPs (snoRNPs) involved in the chemical modification of residues in the vicinity of the peptidyl transferase centre []. The protein has also been referred to as Urb1, and this domain at the N-terminal is one of several conserved regions along the length.
Probab=44.89 E-value=1.3e+02 Score=31.19 Aligned_cols=52 Identities=17% Similarity=0.238 Sum_probs=41.3
Q ss_pred HHHHHHHhCCCCHHHHHHHHHHHHHHHh-cccchhhhhhcchHHHH-HHHHHhc
Q 011515 40 VKGIKKRIGSRNSKVQLLALTLLETIIK-NCGDIVHMHVAEKNVLH-EMVKIAR 91 (484)
Q Consensus 40 vraIrKRL~s~np~vqllAL~LLE~cVK-NCG~~Fh~eVask~FLn-eLvkLv~ 91 (484)
++.|-+-|.+..+..+.-||.||-.+|. +.|.....-+..++|-. .|.+++.
T Consensus 58 ~k~lyr~L~~~~~~~~~~~LrLL~~iv~f~~g~~a~~v~~~fd~~~~~l~kll~ 111 (330)
T PF11707_consen 58 LKLLYRSLSSSKPSLTNPALRLLTAIVSFDGGALAREVLRSFDFSLKSLPKLLT 111 (330)
T ss_pred HHHHHHHhCcCcHHHHHHHHHHHHHHHccCCHHHHHHHHHhcCCchhhHHHHhc
Confidence 6677777777889999999999999999 98877776666777764 4677764
No 59
>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=43.55 E-value=85 Score=26.37 Aligned_cols=57 Identities=11% Similarity=0.287 Sum_probs=35.1
Q ss_pred hhhhhhcchHHHHHHHHHhccC-C---C----------hhHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHH
Q 011515 72 IVHMHVAEKNVLHEMVKIARKK-P---D----------THVKEKILILIDTWQEAFGGPRARYPQYYAAYQELL 131 (484)
Q Consensus 72 ~Fh~eVask~FLneLvkLv~~k-~---d----------~~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk 131 (484)
.++.-+...++++.|+...... + . ..+|.||+.+|..|-+.+..+ +..-...++.|+
T Consensus 32 Tyr~F~tp~~Ll~~L~~ry~~~~~~~~~~~~~~~~~~~~~i~~rv~~~l~~Wi~~~~~d---f~~~~~l~~~l~ 102 (104)
T PF00618_consen 32 TYRSFTTPEELLDKLIQRYNIPPPNGLSQDESWDQDSQEPIRLRVLNVLKYWIENYPDD---FRDDPELLEKLK 102 (104)
T ss_dssp HHHHCS-HHHHHHHHHHHHT---SSS-HHHHT-HHHHHHHHHHHHHHHHHHHHHHHCCC---CHH-HHHHHHHH
T ss_pred HhHhhCCHHHHHHHHHHHhcccCCccccccchhhhhhhHHHHHHHHHHHHHHHHHChHh---hCCCHHHHHHHH
Confidence 3455556677888877766311 1 1 138889999999999999863 433333444443
No 60
>smart00543 MIF4G Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)
Probab=43.51 E-value=95 Score=28.53 Aligned_cols=70 Identities=11% Similarity=0.200 Sum_probs=47.1
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCC---HHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHh
Q 011515 20 AMNIEICDMLNHDPGQAKDVVKGIKKRIGSRN---SKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIA 90 (484)
Q Consensus 20 ~~ileICD~In~~~~~akeAvraIrKRL~s~n---p~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv 90 (484)
+.+.=||++.+..-.........|+.-+...+ +......+.++=.++..||..+... ..+++++++...+
T Consensus 98 ~~i~fl~eL~~~~~i~~~~i~~~l~~ll~~~~~~~~~~~~~~ve~l~~lL~~~G~~l~~~-~~~~~~~~~l~~l 170 (200)
T smart00543 98 GLVRFLGELYNFQVLTSKIILELLKELLNDLTKLDPPRSDFSVECLLSLLPTCGKDLERE-KSPKLLDEILERL 170 (200)
T ss_pred hHHHHHHHHHHcccCcHHHHHHHHHHHHhccCCCCCCCcHHHHHHHHHHHHHhhHHHcCc-ccHHHHHHHHHHH
Confidence 34556899999888877777777776665432 2234567788888889999887742 3455666655443
No 61
>PF12783 Sec7_N: Guanine nucleotide exchange factor in Golgi transport N-terminal
Probab=42.78 E-value=1.1e+02 Score=28.21 Aligned_cols=63 Identities=22% Similarity=0.346 Sum_probs=40.2
Q ss_pred CHHHHHHHHHHHHHHHhcccchhhhhh--------cchHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHhC
Q 011515 51 NSKVQLLALTLLETIIKNCGDIVHMHV--------AEKNVLHEMVKIARKKPDTHVKEKILILIDTWQEAFG 114 (484)
Q Consensus 51 np~vqllAL~LLE~cVKNCG~~Fh~eV--------ask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~aF~ 114 (484)
+......+|.+|+.+++|+|..|...- -+.++..-|.+.+.. .+..|-.+.+.++..--..|+
T Consensus 35 ~~~~k~l~LeLl~~iL~~~~~~f~~~~~~~~l~~~lk~~l~~~Ll~~~~~-~~~~i~~~slri~~~l~~~~~ 105 (168)
T PF12783_consen 35 DERSKLLSLELLESILENHGSVFRSSEEHPSLINLLKDDLCPALLKNLSS-SDFPIFSRSLRIFLTLLSRFR 105 (168)
T ss_pred hHHHHHHHHHHHHHHHHhCHHHHhCCcchHHHHHHHHHHHHHHHHHHHhh-hhhHHHHHHHHHHHHHHHHHH
Confidence 455677999999999999999887311 122233333333333 236777777777776666664
No 62
>COG4477 EzrA Negative regulator of septation ring formation [Cell division and chromosome partitioning]
Probab=41.47 E-value=5.1e+02 Score=29.34 Aligned_cols=41 Identities=20% Similarity=0.344 Sum_probs=36.0
Q ss_pred hHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHhcCCCCCC
Q 011515 97 HVKEKILILIDTWQEAFGGPRARYPQYYAAYQELLRAGAVFPQR 140 (484)
Q Consensus 97 ~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~kGi~FP~~ 140 (484)
...++|=.||......+++ ++..+...|+.|+.+||.||..
T Consensus 211 ~~~e~IP~L~~e~~~~lP~---ql~~Lk~Gyr~m~~~gY~l~~~ 251 (570)
T COG4477 211 SIMERIPSLLAELQTELPG---QLQDLKAGYRDMKEEGYHLEHV 251 (570)
T ss_pred HHHHHHHHHHHHHHhhchH---HHHHHHHHHHHHHHccCCcccc
Confidence 5778888899999999875 5889999999999999999964
No 63
>PF05004 IFRD: Interferon-related developmental regulator (IFRD); InterPro: IPR007701 Interferon-related developmental regulator (IFRD1) is the human homologue of the Rattus norvegicus early response protein PC4 and its murine homologue TIS7 []. The exact function of IFRD1 is unknown but it has been shown that PC4 is necessary for muscle differentiation and that it might have a role in signal transduction. This entry also contains IFRD2 and its murine equivalent SKMc15, which are highly expressed soon after gastrulation and in the hepatic primordium, suggesting an involvement in early hematopoiesis [].
Probab=40.86 E-value=1.9e+02 Score=30.00 Aligned_cols=67 Identities=13% Similarity=0.169 Sum_probs=45.0
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHHHHHHHHhccc--chhhhhhcchHHHHHHHHHhccCC-ChhHHHHHHHHH
Q 011515 38 DVVKGIKKRIGSRNSKVQLLALTLLETIIKNCG--DIVHMHVAEKNVLHEMVKIARKKP-DTHVKEKILILI 106 (484)
Q Consensus 38 eAvraIrKRL~s~np~vqllAL~LLE~cVKNCG--~~Fh~eVask~FLneLvkLv~~k~-d~~VkeKiLeLI 106 (484)
..+..+.|=|+.+..+++.+|+.++..+.-..| ..-+. |- +++...|.+++.... ...+|..++..+
T Consensus 86 tL~~~~~k~lkkg~~~E~~lA~~~l~Ll~ltlg~g~~~~e-i~-~~~~~~L~~~l~d~s~~~~~R~~~~~aL 155 (309)
T PF05004_consen 86 TLLDALLKSLKKGKSEEQALAARALALLALTLGAGEDSEE-IF-EELKPVLKRILTDSSASPKARAACLEAL 155 (309)
T ss_pred HHHHHHHHHhccCCHHHHHHHHHHHHHHhhhcCCCccHHH-HH-HHHHHHHHHHHhCCccchHHHHHHHHHH
Confidence 346667777888888999999999999988865 44332 22 456667777777543 345666555433
No 64
>KOG1820 consensus Microtubule-associated protein [Cytoskeleton]
Probab=39.87 E-value=1.9e+02 Score=34.25 Aligned_cols=91 Identities=15% Similarity=0.263 Sum_probs=67.6
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHh-c--cCCCh
Q 011515 20 AMNIEICDMLNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIA-R--KKPDT 96 (484)
Q Consensus 20 ~~ileICD~In~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv-~--~k~d~ 96 (484)
+.+..+||.|-. ....-...++|.--++++||..-..++.+|+-|++.-|. ....++-++.++..+ + +.++.
T Consensus 354 d~l~~~~d~~~n-s~~l~~~~~~I~e~lk~knp~~k~~~~~~l~r~~~~~~~----~~~~~~t~~~l~p~~~~~~~D~~~ 428 (815)
T KOG1820|consen 354 DALLKALDAILN-STPLSKMSEAILEALKGKNPQIKGECLLLLDRKLRKLGP----KTVEKETVKTLVPHLIKHINDTDK 428 (815)
T ss_pred HHHHHHHHHHHh-cccHHHHHHHHHHHhcCCChhhHHHHHHHHHHHHhhcCC----cCcchhhHHHHhHHHhhhccCCcH
Confidence 445667777665 334567888888899999999999999999999999985 222334455555433 2 12578
Q ss_pred hHHHHHHHHHHHHHHHhCC
Q 011515 97 HVKEKILILIDTWQEAFGG 115 (484)
Q Consensus 97 ~VkeKiLeLIq~Wa~aF~~ 115 (484)
.||.-.++.+-.-..-|+.
T Consensus 429 ~VR~Aa~e~~~~v~k~~Ge 447 (815)
T KOG1820|consen 429 DVRKAALEAVAAVMKVHGE 447 (815)
T ss_pred HHHHHHHHHHHHHHHHhhH
Confidence 9999999999999888864
No 65
>PF11698 V-ATPase_H_C: V-ATPase subunit H; InterPro: IPR011987 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. This entry represents the C-terminal domain of subunit H (also known as Vma13p) found in the V1 complex of V-ATPases. This subunit has a regulatory function, being responsible for activating ATPase activity and coupling ATPase activity to proton flow []. The yeast enzyme contains five motifs similar to the HEAT or Armadillo repeats seen in the importins, and can be divided into two distinct domains: a large N-terminal domain consisting of stacked alpha helices, and a smaller C-terminal alpha-helical domain with a similar superhelical topology to an armadillo repeat []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0015991 ATP hydrolysis coupled proton transport, 0000221 vacuolar proton-transporting V-type ATPase, V1 domain; PDB: 1HO8_A.
Probab=39.78 E-value=1.1e+02 Score=27.74 Aligned_cols=75 Identities=9% Similarity=0.159 Sum_probs=46.0
Q ss_pred CCHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHHH
Q 011515 34 GQAKDVVKGIKKRI-GSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTWQ 110 (484)
Q Consensus 34 ~~akeAvraIrKRL-~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa 110 (484)
++--+.+|.|.+-| .+.++.+..-|+.=|..+|+..... +..|..-..-..+-+++. +.+.+||..+|..+|.|=
T Consensus 39 ~~~~~llk~L~~lL~~s~d~~~laVac~Dig~~vr~~p~g-r~ii~~lg~K~~vM~Lm~-h~d~eVr~eAL~avQklm 114 (119)
T PF11698_consen 39 ENNFELLKKLIKLLDKSDDPTTLAVACHDIGEFVRHYPNG-RNIIEKLGAKERVMELMN-HEDPEVRYEALLAVQKLM 114 (119)
T ss_dssp SGGGHHHHHHHHHH-SHHHHHHHHHHHHHHHHHHHH-GGG-HHHHHHHSHHHHHHHHTS--SSHHHHHHHHHHHHHHH
T ss_pred HcccHHHHHHHHHHccCCCcceeehhhcchHHHHHHChhH-HHHHHhcChHHHHHHHhc-CCCHHHHHHHHHHHHHHH
Confidence 34456778888888 5567777777888888888876321 111211111122223333 478999999999998763
No 66
>PF10508 Proteasom_PSMB: Proteasome non-ATPase 26S subunit; InterPro: IPR019538 The 26S proteasome is an enzymatic complex that degrades ubiquitinated proteins in eukaryotic cells. 26S proteasome non-ATPase regulatory subunit 5 is one of a number of chaperones that are involved in the assembly of the proteasome. The chaperones dissociate before 26S proteasome formation is complete [].; GO: 0044183 protein binding involved in protein folding
Probab=39.37 E-value=2.3e+02 Score=31.33 Aligned_cols=92 Identities=22% Similarity=0.194 Sum_probs=54.3
Q ss_pred CHHHHHHHHHHHhCCCCC-HHHHHHHHHHHhCCC----------------------CHHHHHHHHHHHHHHHhcccchhh
Q 011515 18 DWAMNIEICDMLNHDPGQ-AKDVVKGIKKRIGSR----------------------NSKVQLLALTLLETIIKNCGDIVH 74 (484)
Q Consensus 18 Dw~~ileICD~In~~~~~-akeAvraIrKRL~s~----------------------np~vqllAL~LLE~cVKNCG~~Fh 74 (484)
+-+.+..|+..+...... ++.|+++|++=.++. +..+.++.+.++-.+.+.....|.
T Consensus 117 ~~~l~~~i~~~L~~~d~~Va~~A~~~L~~l~~~~~~~~~l~~~~~~~~L~~l~~~~~~~vR~Rv~el~v~i~~~S~~~~~ 196 (503)
T PF10508_consen 117 DNELLPLIIQCLRDPDLSVAKAAIKALKKLASHPEGLEQLFDSNLLSKLKSLMSQSSDIVRCRVYELLVEIASHSPEAAE 196 (503)
T ss_pred CccHHHHHHHHHcCCcHHHHHHHHHHHHHHhCCchhHHHHhCcchHHHHHHHHhccCHHHHHHHHHHHHHHHhcCHHHHH
Confidence 334556677777655443 566666666555443 333333333333333333333332
Q ss_pred hhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHHHH
Q 011515 75 MHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTWQE 111 (484)
Q Consensus 75 ~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~ 111 (484)
.+.+..|++.+++.++. .|.-||--++++|...+.
T Consensus 197 -~~~~sgll~~ll~eL~~-dDiLvqlnalell~~La~ 231 (503)
T PF10508_consen 197 -AVVNSGLLDLLLKELDS-DDILVQLNALELLSELAE 231 (503)
T ss_pred -HHHhccHHHHHHHHhcC-ccHHHHHHHHHHHHHHHc
Confidence 23335677777777776 688899999999999987
No 67
>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=39.25 E-value=76 Score=26.68 Aligned_cols=73 Identities=15% Similarity=0.180 Sum_probs=46.8
Q ss_pred hHHHHHHHcCCCCCCcCHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCC----C-----------HHHHHHHHHHHHHHH
Q 011515 2 VNSMVDRATSDMLIGPDWAMNIEICDMLNHDPGQAKDVVKGIKKRIGSR----N-----------SKVQLLALTLLETII 66 (484)
Q Consensus 2 v~~lIekATse~l~~~Dw~~ileICD~In~~~~~akeAvraIrKRL~s~----n-----------p~vqllAL~LLE~cV 66 (484)
+++||+++|++.... |-. .++..=+-=..-..+.+.+..|..|.... . ..++++-+.+|-.-|
T Consensus 7 l~~Li~~L~~~~~~~-d~~-f~~~FllTyr~F~tp~~Ll~~L~~ry~~~~~~~~~~~~~~~~~~~~~i~~rv~~~l~~Wi 84 (104)
T PF00618_consen 7 LEKLIERLTSSFNSD-DEE-FVDTFLLTYRSFTTPEELLDKLIQRYNIPPPNGLSQDESWDQDSQEPIRLRVLNVLKYWI 84 (104)
T ss_dssp HHHHHHHHCHC-SS--HHH-HHHHHHHHHHHCS-HHHHHHHHHHHHT---SSS-HHHHT-HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhcccccC-CHH-HHHHHHHHhHhhCCHHHHHHHHHHHhcccCCccccccchhhhhhhHHHHHHHHHHHHHHH
Confidence 688999999884433 222 22222222244567899999999999421 1 126778889999999
Q ss_pred hcccchhhhh
Q 011515 67 KNCGDIVHMH 76 (484)
Q Consensus 67 KNCG~~Fh~e 76 (484)
++|...|+..
T Consensus 85 ~~~~~df~~~ 94 (104)
T PF00618_consen 85 ENYPDDFRDD 94 (104)
T ss_dssp HHHCCCCHH-
T ss_pred HHChHhhCCC
Confidence 9998888764
No 68
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=36.79 E-value=75 Score=26.80 Aligned_cols=70 Identities=14% Similarity=0.106 Sum_probs=43.4
Q ss_pred HHHHHhcccchhhhhhcchHHHHHHHHHhccCC-ChhHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHhc
Q 011515 62 LETIIKNCGDIVHMHVAEKNVLHEMVKIARKKP-DTHVKEKILILIDTWQEAFGGPRARYPQYYAAYQELLRAG 134 (484)
Q Consensus 62 LE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~-d~~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~kG 134 (484)
|+.+..|-|..+..-.-.=.|-+.=+..+...+ ...+++++.+||..|....+.. ...+..+.+.|++-|
T Consensus 5 l~~l~~~lG~~Wk~lar~LG~s~~eI~~ie~~~~r~~~~eq~~~mL~~W~~r~g~~---~ATv~~L~~aL~~~~ 75 (86)
T cd08777 5 LDLLRENLGKKWKRCARKLGFTESEIEEIDHDYERDGLKEKVHQMLHKWKMKEGSK---GATVGKLAQALEGCI 75 (86)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHhcccCCHHHHHHHHHHHHHHccCCC---CcHHHHHHHHHHHcc
Confidence 456667777766644333344444344444332 3458999999999999987531 234666677776544
No 69
>PRK01005 V-type ATP synthase subunit E; Provisional
Probab=35.72 E-value=87 Score=30.79 Aligned_cols=61 Identities=11% Similarity=0.009 Sum_probs=48.4
Q ss_pred HHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhccCC-Chh-HHHHHHHHHHHHHHH
Q 011515 52 SKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKP-DTH-VKEKILILIDTWQEA 112 (484)
Q Consensus 52 p~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~-d~~-VkeKiLeLIq~Wa~a 112 (484)
..+.-++..-++.-.+++-.....+|...-|-..+.+++.... |++ +++.|++++..|...
T Consensus 63 e~ek~r~~s~a~l~~R~~~l~aKqevi~~vf~~a~~~lv~~~~~d~~~l~~lI~~~v~~~~~~ 125 (207)
T PRK01005 63 DQKLKQGESALVQAGKRSLESLKQAVENKIFRESLGEWLEHVLTDPEVSAKLIQALVQAIEAQ 125 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHhhc
Confidence 3444478888888888888888888888888888999988653 665 677788899999875
No 70
>smart00005 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
Probab=35.48 E-value=73 Score=25.89 Aligned_cols=69 Identities=13% Similarity=0.199 Sum_probs=39.6
Q ss_pred HHHHHhc-ccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHhc
Q 011515 62 LETIIKN-CGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTWQEAFGGPRARYPQYYAAYQELLRAG 134 (484)
Q Consensus 62 LE~cVKN-CG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~kG 134 (484)
+..+.++ -|..+..-...-.|-..-+.-++...+..+++++.+||..|....+.. ..+..+.+.|++-|
T Consensus 8 ~~~l~~~~~g~~W~~la~~Lg~~~~~i~~i~~~~~~~~~~~~~~lL~~W~~~~g~~----at~~~L~~aL~~~~ 77 (88)
T smart00005 8 LAKLLDHPLGLDWRELARKLGLSEADIDQIRTEAPRDLAEQSVQLLRLWEQREGKN----ATLGTLLEALRKMG 77 (88)
T ss_pred HHHHHcCccchHHHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHccchh----hHHHHHHHHHHHcC
Confidence 3444444 455544322222442332333332223368999999999999987642 35667777777765
No 71
>KOG2075 consensus Topoisomerase TOP1-interacting protein BTBD1 [Function unknown]
Probab=35.20 E-value=1.4e+02 Score=33.17 Aligned_cols=96 Identities=13% Similarity=0.132 Sum_probs=63.2
Q ss_pred cCHHHHHHHHHHHhCCCCC--HHHHHHHHHHHhCCCCHHHHHHH-------HHHHHHHHhcccchhhhhhcchHH-----
Q 011515 17 PDWAMNIEICDMLNHDPGQ--AKDVVKGIKKRIGSRNSKVQLLA-------LTLLETIIKNCGDIVHMHVAEKNV----- 82 (484)
Q Consensus 17 ~Dw~~ileICD~In~~~~~--akeAvraIrKRL~s~np~vqllA-------L~LLE~cVKNCG~~Fh~eVask~F----- 82 (484)
.+-+.+|.+|+..++--+. .++||+.|+|+|.-.|.=.-+-+ =.|+..|++.-...|-..+..+.|
T Consensus 185 ~~~dtvi~tl~~AkKY~VpaLer~CVkflr~~l~~~naf~~L~q~A~lf~ep~Li~~c~e~id~~~~~al~~EGf~did~ 264 (521)
T KOG2075|consen 185 LAADTVITTLYAAKKYLVPALERQCVKFLRKNLMADNAFLELFQRAKLFDEPSLISICLEVIDKSFEDALTPEGFCDIDS 264 (521)
T ss_pred hhHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhcCChHHHHHHHHHHHhhcCHHHHHHHHHHhhhHHHhhhCccceeehhh
Confidence 4556788889888886665 58999999999988765444444 156667777666666555544333
Q ss_pred -HHHHHHHhccCCChhHHH-HHHHHHHHHHHHh
Q 011515 83 -LHEMVKIARKKPDTHVKE-KILILIDTWQEAF 113 (484)
Q Consensus 83 -LneLvkLv~~k~d~~Vke-KiLeLIq~Wa~aF 113 (484)
++.++.+++.+. .++++ ++.+.+..|...=
T Consensus 265 ~~dt~~evl~r~~-l~~~e~~lfeA~lkw~~~e 296 (521)
T KOG2075|consen 265 TRDTYEEVLRRDT-LEAREFRLFEAALKWAEAE 296 (521)
T ss_pred HHHHHHHHHhhcc-cchhHHHHHHHHHhhccCc
Confidence 444555555433 23444 7888888898743
No 72
>PF10508 Proteasom_PSMB: Proteasome non-ATPase 26S subunit; InterPro: IPR019538 The 26S proteasome is an enzymatic complex that degrades ubiquitinated proteins in eukaryotic cells. 26S proteasome non-ATPase regulatory subunit 5 is one of a number of chaperones that are involved in the assembly of the proteasome. The chaperones dissociate before 26S proteasome formation is complete [].; GO: 0044183 protein binding involved in protein folding
Probab=35.09 E-value=2.3e+02 Score=31.32 Aligned_cols=92 Identities=17% Similarity=0.256 Sum_probs=69.8
Q ss_pred CHHHHHHHHHHHhC--CCCC----HHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhc
Q 011515 18 DWAMNIEICDMLNH--DPGQ----AKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIAR 91 (484)
Q Consensus 18 Dw~~ileICD~In~--~~~~----akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~ 91 (484)
+-+.+..+|++|++ +... .......|.+=|.|.++.|..+++..|.-|+.+-+. ....+.+.+++..+..++.
T Consensus 51 ~~e~v~~~~~iL~~~l~~~~~~~l~~~~~~~L~~gL~h~~~~Vr~l~l~~l~~~~~~~~~-~~~~~~~~~l~~~i~~~L~ 129 (503)
T PF10508_consen 51 NREQVELICDILKRLLSALSPDSLLPQYQPFLQRGLTHPSPKVRRLALKQLGRIARHSEG-AAQLLVDNELLPLIIQCLR 129 (503)
T ss_pred ChHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCCHH-HHHHhcCccHHHHHHHHHc
Confidence 55566677777664 2222 345666778888999999999999999999887654 4556777888888888776
Q ss_pred cCCChhHHHHHHHHHHHHHH
Q 011515 92 KKPDTHVKEKILILIDTWQE 111 (484)
Q Consensus 92 ~k~d~~VkeKiLeLIq~Wa~ 111 (484)
. ++..|.+.+..+|..-..
T Consensus 130 ~-~d~~Va~~A~~~L~~l~~ 148 (503)
T PF10508_consen 130 D-PDLSVAKAAIKALKKLAS 148 (503)
T ss_pred C-CcHHHHHHHHHHHHHHhC
Confidence 5 578999999998888774
No 73
>KOG1077 consensus Vesicle coat complex AP-2, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=34.48 E-value=1e+02 Score=35.83 Aligned_cols=73 Identities=11% Similarity=0.240 Sum_probs=51.9
Q ss_pred CHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHHHH
Q 011515 35 QAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTWQE 111 (484)
Q Consensus 35 ~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~ 111 (484)
.-.-|+..|.+-|.++-.+.-++||+-+-.|.. ..|-...-++. .+.++..++...|..||+|+++|++...+
T Consensus 326 ll~~~~~~Lg~fls~rE~NiRYLaLEsm~~L~s---s~~s~davK~h-~d~Ii~sLkterDvSirrravDLLY~mcD 398 (938)
T KOG1077|consen 326 LLSRAVNQLGQFLSHRETNIRYLALESMCKLAS---SEFSIDAVKKH-QDTIINSLKTERDVSIRRRAVDLLYAMCD 398 (938)
T ss_pred HHHHHHHHHHHHhhcccccchhhhHHHHHHHHh---ccchHHHHHHH-HHHHHHHhccccchHHHHHHHHHHHHHhc
Confidence 346688888999999999999999865444433 23443444344 77777777766788999999999887653
No 74
>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=34.31 E-value=1e+02 Score=20.48 Aligned_cols=30 Identities=17% Similarity=0.275 Sum_probs=25.3
Q ss_pred HHHHHHHhCCCCHHHHHHHHHHHHHHHhcc
Q 011515 40 VKGIKKRIGSRNSKVQLLALTLLETIIKNC 69 (484)
Q Consensus 40 vraIrKRL~s~np~vqllAL~LLE~cVKNC 69 (484)
+-.|.+-+.+++++|...|..-|..+++.|
T Consensus 2 lp~l~~~l~D~~~~VR~~a~~~l~~i~~~~ 31 (31)
T PF02985_consen 2 LPILLQLLNDPSPEVRQAAAECLGAIAEHC 31 (31)
T ss_dssp HHHHHHHHT-SSHHHHHHHHHHHHHHHHTS
T ss_pred HHHHHHHcCCCCHHHHHHHHHHHHHHHhhC
Confidence 346778889999999999999999999887
No 75
>PF12333 Ipi1_N: Rix1 complex component involved in 60S ribosome maturation; InterPro: IPR024679 This domain is found in IPI1, which is a component of the Rix1 complex involved in pre-rRNA-processing [, ]. It is also found in testis-expressed sequence 10 protein, a nuclear membrane protein, which is a component of the MLL1/MLL complex [].
Probab=33.88 E-value=3.1e+02 Score=23.63 Aligned_cols=52 Identities=10% Similarity=0.139 Sum_probs=36.7
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhc
Q 011515 39 VVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIAR 91 (484)
Q Consensus 39 AvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~ 91 (484)
.+-.|+-=+.|-.+.++.-||.+||.|++.|+..+-..- -.+.++-+..++.
T Consensus 12 l~~~i~sAMTHi~~~Ir~dsl~~L~~lL~~~p~~~~~~~-~~kil~~f~~ll~ 63 (102)
T PF12333_consen 12 LMLYISSAMTHISPDIREDSLKFLDLLLEHAPDELCSGG-WVKILPNFLDLLG 63 (102)
T ss_pred HHHHHHHHHHhCCHHHHHhHHHHHHHHHHHCChHhHhhh-HHHHHHHHHHHHC
Confidence 344566667788999999999999999999998722221 2345555666654
No 76
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=33.81 E-value=1.1e+02 Score=24.35 Aligned_cols=66 Identities=11% Similarity=0.171 Sum_probs=35.1
Q ss_pred HHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHhc
Q 011515 64 TIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTWQEAFGGPRARYPQYYAAYQELLRAG 134 (484)
Q Consensus 64 ~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~kG 134 (484)
.+-...|..+..-...=.|-+.-+..+....+. +++++.++|..|....+.. ..+..++..|++-|
T Consensus 6 ~l~~~~~~~Wk~La~~Lg~~~~~i~~i~~~~~~-~~~~~~~~L~~W~~~~~~~----at~~~L~~aL~~~~ 71 (83)
T PF00531_consen 6 LLAEDLGSDWKRLARKLGLSESEIENIEEENPD-LREQTYEMLQRWRQREGPN----ATVDQLIQALRDIG 71 (83)
T ss_dssp HHHHSHSTCHHHHHHHTTS-HHHHHHHHHHSTS-HHHHHHHHHHHHHHHHGST----SSHHHHHHHHHHTT
T ss_pred HHhhcchhhHHHHHHHhCcCHHHHHHHHHhCCC-hHHHHHHHHHHHHHhcCCC----CcHHHHHHHHHHCC
Confidence 333444444443222223433333333323333 9999999999999995442 23455566665543
No 77
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-associati
Probab=33.64 E-value=97 Score=25.63 Aligned_cols=68 Identities=13% Similarity=0.148 Sum_probs=37.9
Q ss_pred HHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHhc
Q 011515 63 ETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTWQEAFGGPRARYPQYYAAYQELLRAG 134 (484)
Q Consensus 63 E~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~kG 134 (484)
..+.++-|..+..-...=.|-..=+..++...+..+.+++..+|..|.+..+.. ..+..+.+.|++-|
T Consensus 8 ~~ia~~lG~dW~~LAr~Lg~~~~dI~~i~~~~~~~~~eq~~~mL~~W~~r~g~~----at~~~L~~AL~~i~ 75 (84)
T cd08317 8 ADISNLLGSDWPQLARELGVSETDIDLIKAENPNSLAQQAQAMLKLWLEREGKK----ATGNSLEKALKKIG 75 (84)
T ss_pred HHHHHHHhhHHHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHhcCCc----chHHHHHHHHHHcC
Confidence 344455555554333322333322233333333457899999999999987642 33455666666544
No 78
>KOG1062 consensus Vesicle coat complex AP-1, gamma subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=33.57 E-value=1.9e+02 Score=34.06 Aligned_cols=103 Identities=12% Similarity=0.184 Sum_probs=66.7
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcc---cchhhhhhcchHHHHHHHHHhccC----
Q 011515 21 MNIEICDMLNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNC---GDIVHMHVAEKNVLHEMVKIARKK---- 93 (484)
Q Consensus 21 ~ileICD~In~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNC---G~~Fh~eVask~FLneLvkLv~~k---- 93 (484)
.++-..-+|++.++-...-+-..+++|..+++-|-+-+|.++-.+.+.. =..|.. ....|+..|+.++..+
T Consensus 162 A~Lca~r~irK~P~l~e~f~~~~~~lL~ek~hGVL~~~l~l~~e~c~~~~~~l~~fr~--l~~~lV~iLk~l~~~~yspe 239 (866)
T KOG1062|consen 162 AALCAVRFIRKVPDLVEHFVIAFRKLLCEKHHGVLIAGLHLITELCKISPDALSYFRD--LVPSLVKILKQLTNSGYSPE 239 (866)
T ss_pred HHHHHHHHHHcCchHHHHhhHHHHHHHhhcCCceeeeHHHHHHHHHhcCHHHHHHHHH--HHHHHHHHHHHHhcCCCCCc
Confidence 3444445566666666666667778888888888888888876666663 224444 2345666666666543
Q ss_pred ------CChhHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHH
Q 011515 94 ------PDTHVKEKILILIDTWQEAFGGPRARYPQYYAAYQELLR 132 (484)
Q Consensus 94 ------~d~~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~ 132 (484)
+|+-.+-|||.++..... ++ +...+.+.++..
T Consensus 240 ydv~gi~dPFLQi~iLrlLriLGq---~d----~daSd~M~DiLa 277 (866)
T KOG1062|consen 240 YDVHGISDPFLQIRILRLLRILGQ---ND----ADASDLMNDILA 277 (866)
T ss_pred cCccCCCchHHHHHHHHHHHHhcC---CC----ccHHHHHHHHHH
Confidence 457799999999887764 22 344555555544
No 79
>PF07531 TAFH: NHR1 homology to TAF; InterPro: IPR003894 The TAF homology (TAFH) or Nervy homology region 1 (NHR1) domain is a domain of 95-100 amino acids present in eukaryotic proteins of the MTG/ETO family and whereof the core ~75-80 residues occur in TAF proteins. The transcription initiation TFIID complex is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). The TAFH/NHR1 domain is named after fruit fly TATA-box-associated factor 110 (TAF110), human TAF105 and TAF130, and the fruit fly protein Nervy, which is a homologue of human MTG8/ETO [, ]. The human eight twenty-one (ETO or MTG8) and related myeloid transforming gene products MTGR1 and MTG16 as well as the Nervy protein contain the NHR1-4 domains. The NHR1/TAFH domain occurs in the N-terminal part of these proteins, while a MYND-type zinc finger forms the NHR4 domain []. The TAFH/NHR1 domain can be involved in protein-protein interactions, e.g in MTG8/ETO with HSP90 and Gfi-1 []. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2P6V_A 2KNH_A 2PP4_A 2H7B_A.
Probab=33.21 E-value=59 Score=28.41 Aligned_cols=33 Identities=24% Similarity=0.440 Sum_probs=27.6
Q ss_pred hHHHHHHHHHhccCCChhHHHHHHHHHHHHHHH
Q 011515 80 KNVLHEMVKIARKKPDTHVKEKILILIDTWQEA 112 (484)
Q Consensus 80 k~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~a 112 (484)
+.||..|+++.+++..++|.+++.+||+..-++
T Consensus 7 k~FL~tLi~las~~~spev~~~Vr~LV~~L~~~ 39 (96)
T PF07531_consen 7 KNFLNTLIQLASDKQSPEVGENVRELVQNLVDG 39 (96)
T ss_dssp HHHHHHHHHHHCCSC-CCHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHhcCCCChHHHHHHHHHHHHHHcC
Confidence 689999999998866778999999999888764
No 80
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=32.37 E-value=64 Score=35.46 Aligned_cols=62 Identities=29% Similarity=0.465 Sum_probs=0.0
Q ss_pred CCCCCCCCcccchhhHhhhhccCCCCCCCCCCCCCCC--CCCCCCCCcccccccCCCCCCcccCCCCCCCCCCCCcc
Q 011515 371 PQPNTPVSSQQNALVLFDMFSDATNAPNSINTQPANM--AGQPNSLAPQFHQQQNFQTPEAGLYQNGTAPNMGSPRY 445 (484)
Q Consensus 371 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 445 (484)
|++++|. |+|| --....+-++.+. +++.+..+|+|+-||..++|++.+|||--..++-.|.|
T Consensus 419 yppp~p~---------f~m~----~~hP~~~~p~~~~g~~~P~~~mpp~~P~~~~pppP~~pp~p~~~~~q~q~~~y 482 (483)
T KOG2236|consen 419 YPPPSPS---------FPMF----QPHPPESNPPANFGQANPFNQMPPAYPHQQSPPPPPPPPPPNSPMNQMQNPSY 482 (483)
T ss_pred CCCCCCC---------CCcc----CCCCCCCCCcccccccCccccCCCCCccccCCCCCCCCCCCCChhhcccCCCC
No 81
>PTZ00429 beta-adaptin; Provisional
Probab=31.97 E-value=2.6e+02 Score=32.77 Aligned_cols=86 Identities=16% Similarity=0.306 Sum_probs=51.0
Q ss_pred cCHHHHHHHHHHHhC----CCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhcc
Q 011515 17 PDWAMNIEICDMLNH----DPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARK 92 (484)
Q Consensus 17 ~Dw~~ileICD~In~----~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~ 92 (484)
.+|..+ .|-+++.. +.....+.+..+..+|+|.|+.|++-|+.++=.+..+|....+.++. ++.-.-|+.|.+
T Consensus 232 ~EW~Qi-~IL~lL~~y~P~~~~e~~~il~~l~~~Lq~~N~AVVl~Aik~il~l~~~~~~~~~~~~~-~rl~~pLv~L~s- 308 (746)
T PTZ00429 232 NEWGQL-YILELLAAQRPSDKESAETLLTRVLPRMSHQNPAVVMGAIKVVANLASRCSQELIERCT-VRVNTALLTLSR- 308 (746)
T ss_pred ChHHHH-HHHHHHHhcCCCCcHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCcCCHHHHHHHH-HHHHHHHHHhhC-
Confidence 477754 24444332 22335678888999999999999999999887777777544444433 233333444432
Q ss_pred CCChhHHHHHHHHH
Q 011515 93 KPDTHVKEKILILI 106 (484)
Q Consensus 93 k~d~~VkeKiLeLI 106 (484)
.+.+||--+|..|
T Consensus 309 -s~~eiqyvaLr~I 321 (746)
T PTZ00429 309 -RDAETQYIVCKNI 321 (746)
T ss_pred -CCccHHHHHHHHH
Confidence 2334444444333
No 82
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=31.79 E-value=1.2e+02 Score=25.69 Aligned_cols=69 Identities=16% Similarity=0.167 Sum_probs=45.9
Q ss_pred HHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHhc
Q 011515 62 LETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTWQEAFGGPRARYPQYYAAYQELLRAG 134 (484)
Q Consensus 62 LE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~kG 134 (484)
++.+.+|-|.........-.|-..=+..++...+..+.+++..++..|....+. ...+..+++.|++-|
T Consensus 7 l~~Ia~~LG~dW~~Lar~L~vs~~dI~~I~~e~p~~l~~Q~~~~L~~W~~r~g~----~At~~~L~~AL~~i~ 75 (84)
T cd08805 7 MAVIREHLGLSWAELARELQFSVEDINRIRVENPNSLLEQSTALLNLWVDREGE----NAKMSPLYPALYSID 75 (84)
T ss_pred HHHHHHHhcchHHHHHHHcCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHHhcCc----cchHHHHHHHHHHCC
Confidence 556677778777655554455543233344333456999999999999998764 345667788887654
No 83
>PF14500 MMS19_N: Dos2-interacting transcription regulator of RNA-Pol-II
Probab=31.31 E-value=2.4e+02 Score=28.58 Aligned_cols=77 Identities=10% Similarity=0.243 Sum_probs=50.5
Q ss_pred HHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHh
Q 011515 36 AKDVVKGIKKRI--GSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTWQEAF 113 (484)
Q Consensus 36 akeAvraIrKRL--~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~aF 113 (484)
+...++.|-+++ ++.-..+-+..+.||+.++.|-....+ .++ .+|+..++.++....|++---.+.+++..-...|
T Consensus 78 ~~~i~~~l~~~~~~q~~~q~~R~~~~~ll~~l~~~~~~~l~-~~~-~~fv~~~i~~~~gEkDPRnLl~~F~l~~~i~~~~ 155 (262)
T PF14500_consen 78 AVKILRSLFQNVDVQSLPQSTRYAVYQLLDSLLENHREALQ-SMG-DDFVYGFIQLIDGEKDPRNLLLSFKLLKVILQEF 155 (262)
T ss_pred HHHHHHHHHHhCChhhhhHHHHHHHHHHHHHHHHHhHHHHH-hch-hHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHhc
Confidence 334444444433 234556667888999999999765553 444 6899999999987777766556666666555555
Q ss_pred C
Q 011515 114 G 114 (484)
Q Consensus 114 ~ 114 (484)
.
T Consensus 156 ~ 156 (262)
T PF14500_consen 156 D 156 (262)
T ss_pred c
Confidence 4
No 84
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=31.24 E-value=8e+02 Score=27.58 Aligned_cols=98 Identities=19% Similarity=0.241 Sum_probs=56.8
Q ss_pred HHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhh---c------chHHHHHHHHHhccCCChhHHHHHHHHHH
Q 011515 37 KDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHV---A------EKNVLHEMVKIARKKPDTHVKEKILILID 107 (484)
Q Consensus 37 keAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eV---a------sk~FLneLvkLv~~k~d~~VkeKiLeLIq 107 (484)
++--+.+||.|...+ +.=--|+.-||..+.+-...|-.-. . .++.+..+..-+.. =....++|=.++.
T Consensus 146 ~~~y~~~rk~ll~~~-~~~G~a~~~le~~l~~~e~~f~~f~~l~~~Gd~~~A~e~l~~l~~~~~~--l~~~~~~iP~l~~ 222 (569)
T PRK04778 146 KDLYRELRKSLLANR-FSFGPALDELEKQLENLEEEFSQFVELTESGDYVEAREILDQLEEELAA--LEQIMEEIPELLK 222 (569)
T ss_pred HHHHHHHHHHHHhcC-ccccchHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHH
Confidence 444445555553211 1112466777777777766554311 1 12333333221111 1245556667778
Q ss_pred HHHHHhCCCCCCchHHHHHHHHHHHhcCCCCCC
Q 011515 108 TWQEAFGGPRARYPQYYAAYQELLRAGAVFPQR 140 (484)
Q Consensus 108 ~Wa~aF~~~~~~~~~i~~~Y~~Lk~kGi~FP~~ 140 (484)
.-...|++ .+..+...|+.|+.+||.|+..
T Consensus 223 ~~~~~~P~---ql~el~~gy~~m~~~gy~~~~~ 252 (569)
T PRK04778 223 ELQTELPD---QLQELKAGYRELVEEGYHLDHL 252 (569)
T ss_pred HHHHHhhH---HHHHHHHHHHHHHHcCCCCCCC
Confidence 88888875 5888999999999999999854
No 85
>PF04740 LXG: LXG domain of WXG superfamily; InterPro: IPR006829 This group of putative transposases is found in Gram-positive bacteria, mostly Bacillus members and is thought to be a Cytosolic protein. However, we have also found a Bacillus subtilis bacteriophage SPbetac2 homologue (O64023 from SWISSPROT), possibly arising as a result of horizontal transfer. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=30.96 E-value=4e+02 Score=25.12 Aligned_cols=81 Identities=12% Similarity=0.260 Sum_probs=47.1
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCCccCchHHHH-HHHHHHHHHHHHHHHHhhcc----------------CCHHHHHHHhh
Q 011515 189 IQNARGIMDVLAEMLNALDPNNKEGLRQEVIV-DLVDQCRTYKQRVVHLVNST----------------ADESLLCQGLQ 251 (484)
Q Consensus 189 Le~ak~nv~LL~EML~~~~P~~~e~~d~Eli~-EL~~~Cr~~q~rV~rLI~~~----------------~DEelL~eLL~ 251 (484)
++.....++.+.+-+..+++...-..+.+.++ ++-..++.+...+..+...+ ....+...+-.
T Consensus 70 ~~~~~~~l~~~~~~~~~vd~~~~a~i~e~~L~~el~~~l~~~~~~~~~~~~~~~~~~~~vsdiv~~~~~~~~~~~~~~~~ 149 (204)
T PF04740_consen 70 LEEYQEALKFIKDFQSEVDSSSNAIIDEDFLESELKKKLNQLKEQIEDLQDEINSILSSVSDIVSLPKPSSSSFIDSLEK 149 (204)
T ss_pred HHHHHHHHHhHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccchHHHHhhccchHHHHHHHHHH
Confidence 34444445666665656654333335566666 66666666666555444321 24556666667
Q ss_pred hhHHHHHHHHHHHhhhcC
Q 011515 252 LNDDLQRLLAKHESFASG 269 (484)
Q Consensus 252 aNDeL~~vL~rYe~l~~g 269 (484)
+...|+..+++...|...
T Consensus 150 ~~~~l~~~lekL~~fd~~ 167 (204)
T PF04740_consen 150 AKKKLQETLEKLRAFDQQ 167 (204)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 777777777777777553
No 86
>smart00549 TAFH TAF homology. Domain in Drosophila nervy, CBFA2T1, human TAF105, human TAF130, and Drosophila TAF110. Also known as nervy homology region 1 (NHR1).
Probab=30.90 E-value=76 Score=27.51 Aligned_cols=33 Identities=15% Similarity=0.303 Sum_probs=27.2
Q ss_pred hHHHHHHHHHhccCCChhHHHHHHHHHHHHHHH
Q 011515 80 KNVLHEMVKIARKKPDTHVKEKILILIDTWQEA 112 (484)
Q Consensus 80 k~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~a 112 (484)
++|+..|+++.++...++|-+++.+||+..-++
T Consensus 6 k~FL~tLi~ls~~~~qpe~~~~Vr~LV~~L~~~ 38 (92)
T smart00549 6 KRFLTTLIQLSNDISQPEVAERVRTLVLGLVNG 38 (92)
T ss_pred HHHHHHHHHHhcCCCcchHHHHHHHHHHHHHhC
Confidence 689999999988755478888888888887765
No 87
>PF14523 Syntaxin_2: Syntaxin-like protein; PDB: 2DNX_A.
Probab=30.37 E-value=2.9e+02 Score=23.03 Aligned_cols=80 Identities=16% Similarity=0.262 Sum_probs=44.5
Q ss_pred HHHHHHHHHHHHHHHHhhcCC-CCCccCchHHHHHHHHHHHHHHHHHHHHhhcc------C--CHHHHHHHhhhhHHHHH
Q 011515 188 EIQNARGIMDVLAEMLNALDP-NNKEGLRQEVIVDLVDQCRTYKQRVVHLVNST------A--DESLLCQGLQLNDDLQR 258 (484)
Q Consensus 188 eLe~ak~nv~LL~EML~~~~P-~~~e~~d~Eli~EL~~~Cr~~q~rV~rLI~~~------~--DEelL~eLL~aNDeL~~ 258 (484)
-|....+++.-|..|+..+-- .+.... -+-|.++...|+.+-..+-+.|... . +-..-...=.+..++..
T Consensus 4 ~l~~in~~v~~l~k~~~~lGt~~Ds~~l-R~~i~~~~~~~~~l~k~~~~~l~~l~~~~~~~~~~~~~k~~~~KL~~df~~ 82 (102)
T PF14523_consen 4 NLFKINQNVSQLEKLVNQLGTPRDSQEL-REKIHQLIQKTNQLIKEISELLKKLNSLSSDRSNDRQQKLQREKLSRDFKE 82 (102)
T ss_dssp HHHHHHHHHHHHHHHHHHH-SSS--HHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHSH----HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhCCccccHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHH
Confidence 467778889999999888731 111111 2334555666665555554444321 1 12222334456677788
Q ss_pred HHHHHHhhhc
Q 011515 259 LLAKHESFAS 268 (484)
Q Consensus 259 vL~rYe~l~~ 268 (484)
+|..|....+
T Consensus 83 ~l~~fq~~q~ 92 (102)
T PF14523_consen 83 ALQEFQKAQR 92 (102)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHH
Confidence 8888877643
No 88
>PF12783 Sec7_N: Guanine nucleotide exchange factor in Golgi transport N-terminal
Probab=29.88 E-value=2.7e+02 Score=25.65 Aligned_cols=71 Identities=13% Similarity=0.192 Sum_probs=52.4
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHH-HhccCC-ChhHHHHHHHHHHHHHH
Q 011515 39 VVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVK-IARKKP-DTHVKEKILILIDTWQE 111 (484)
Q Consensus 39 AvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvk-Lv~~k~-d~~VkeKiLeLIq~Wa~ 111 (484)
..++|-+-+.+.++.+..++|.++-.++.+-+..+..|+ .-|+..+.. ++..+. +..-|.-+|+.+..+-.
T Consensus 74 l~~~Ll~~~~~~~~~i~~~slri~~~l~~~~~~~Lk~el--e~~l~~i~~~il~~~~~~~~~k~~~Le~l~~l~~ 146 (168)
T PF12783_consen 74 LCPALLKNLSSSDFPIFSRSLRIFLTLLSRFRSHLKLEL--EVFLSHIILRILESDNSSLWQKELALEILRELCK 146 (168)
T ss_pred HHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHccCCCcHHHHHHHHHHHHHHHh
Confidence 334444455567799999999999999988877666666 578998777 666543 45677888888888764
No 89
>PF11099 M11L: Apoptosis regulator M11L like; InterPro: IPR021119 This entry includes the poxvirus familes F1 and C10. C10 proteins are apoptosis regulators, which function to modulate the apoptotic cascades and thereby favour productive viral replication. One of these, M11L inhibits mitochondrial-dependent apoptosis by mimicking and competing with host proteins for the binding and blocking of Bak and Bax, two executioner proteins []. The poxvirus F1 family are a family of conserved proteins related to Vaccinia virus protein F1L. They have no known function.; PDB: 2O42_B 2JBY_A 2JBX_B 2VTY_A.
Probab=29.06 E-value=1.6e+02 Score=28.27 Aligned_cols=65 Identities=15% Similarity=0.339 Sum_probs=41.4
Q ss_pred HHHHHHhCCCCC--HHHHHHHHHHHhCC-CCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHH
Q 011515 24 EICDMLNHDPGQ--AKDVVKGIKKRIGS-RNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVK 88 (484)
Q Consensus 24 eICD~In~~~~~--akeAvraIrKRL~s-~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvk 88 (484)
.+||.+..+... -.+....|..=|.+ ..|.|-|-+|+|+-.+++-||..-.......-.+++++.
T Consensus 48 ~mcd~i~~~~~S~~I~~Ikn~v~~~L~~D~rpsVkLAtISLiS~I~~k~~~~~~ti~m~~~l~~dIi~ 115 (167)
T PF11099_consen 48 SMCDIIEANDISYNIDDIKNEVIEILLSDNRPSVKLATISLISIIIEKWGNKNKTIHMDSLLSNDIID 115 (167)
T ss_dssp HHHHHHHCCCCTT-HHHHHHHHHHHCCHT--HHHHHHHHHHHHHHHHHH--HHCCCHHHHHHHHHHHH
T ss_pred HHHHHHhcccccccHHHHHHHHHHHHhccCCCceeehHHHHHHHHHHHHhhccchhhHHHHHHHHHHH
Confidence 389988866544 47777777777774 559999999999999999885433322222233444443
No 90
>KOG3192 consensus Mitochondrial J-type chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=29.05 E-value=1.2e+02 Score=29.05 Aligned_cols=44 Identities=16% Similarity=0.267 Sum_probs=26.8
Q ss_pred hHHHHHHHHHHHHHHHHHHH--Hhh-----------ccCCHHHHHHHhhhhHHHHHH
Q 011515 216 QEVIVDLVDQCRTYKQRVVH--LVN-----------STADESLLCQGLQLNDDLQRL 259 (484)
Q Consensus 216 ~Eli~EL~~~Cr~~q~rV~r--LI~-----------~~~DEelL~eLL~aNDeL~~v 259 (484)
.|-..+|.+.|+.+...+-| ||- .+.|.++|.++|.++|+|.+.
T Consensus 55 ~eqSa~lnkAY~TLk~pL~RA~Yilkl~g~e~~sne~stDpe~Lmevle~~E~IS~~ 111 (168)
T KOG3192|consen 55 SEQSAELNKAYDTLKDPLARARYLLKLKGQEQTSNELSTDPEFLMEVLEYHEAISEM 111 (168)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHhCCCCchhhhccCHHHHHHHHHHHHHHHhc
Confidence 34455666666666655544 221 124778888888888877653
No 91
>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=28.99 E-value=85 Score=23.17 Aligned_cols=52 Identities=13% Similarity=0.287 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHH
Q 011515 52 SKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILI 106 (484)
Q Consensus 52 p~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLI 106 (484)
+.+...|+..|-.+...|+..+...+ .+.+..|.++++. .+..||.....-|
T Consensus 1 p~vR~~A~~aLg~l~~~~~~~~~~~~--~~~~~~L~~~L~d-~~~~VR~~A~~aL 52 (55)
T PF13513_consen 1 PRVRRAAAWALGRLAEGCPELLQPYL--PELLPALIPLLQD-DDDSVRAAAAWAL 52 (55)
T ss_dssp HHHHHHHHHHHHCTTTTTHHHHHHHH--HHHHHHHHHHTTS-SSHHHHHHHHHHH
T ss_pred CHHHHHHHHHHhhHhcccHHHHHHHH--HHHHHHHHHHHcC-CCHHHHHHHHHHH
Confidence 35667778888778888887666533 4677777777765 3458988876544
No 92
>PF08328 ASL_C: Adenylosuccinate lyase C-terminal; InterPro: IPR013539 This domain is found at the C terminus of adenylosuccinate lyase(ASL; PurB in Escherichia coli). It has been identified in bacteria, eukaryotes and archaea and is found together with the lyase domain IPR000362 from INTERPRO. ASL catalyses the cleavage of succinylaminoimidazole carboxamide ribotide to aminoimidazole carboxamide ribotide and fumarate and the cleavage of adenylosuccinate to adenylate and fumarate []. ; GO: 0004018 N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity, 0006188 IMP biosynthetic process; PDB: 2HVG_A 2QGA_C 2PTS_A 2PTR_A 2PTQ_B 3BHG_A 3GZH_A.
Probab=27.93 E-value=1.3e+02 Score=27.20 Aligned_cols=63 Identities=17% Similarity=0.249 Sum_probs=37.9
Q ss_pred HHhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHH
Q 011515 28 MLNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILIL 105 (484)
Q Consensus 28 ~In~~~~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeL 105 (484)
-++...+--.|++..+.+|-+..+|.+++.+|+- |..+-.+.- ++|++.| . .+..+|++++.|
T Consensus 47 dL~~nWeVlaEpIQTvmRr~g~~~pYE~LK~lTR--------g~~it~~~l-~~fI~~L----~--ip~~~k~~L~~l 109 (115)
T PF08328_consen 47 DLDENWEVLAEPIQTVMRRYGIPNPYEKLKELTR--------GKKITKEDL-REFIESL----D--IPEEAKARLLAL 109 (115)
T ss_dssp HHCT-GGGGHHHHHHHHHHTT-SSHHHHHHHHHT--------TS---HHHH-HHHHHTS----S--S-HHHHHHHHH-
T ss_pred HHHHCHHHHHHHHHHHHHHcCCCCHHHHHHHHHc--------CCCCCHHHH-HHHHHhC----C--CCHHHHHHHHhc
Confidence 3455555678999999999999999999999873 443322211 2233322 1 466788887765
No 93
>PLN03200 cellulose synthase-interactive protein; Provisional
Probab=27.06 E-value=2.5e+02 Score=36.71 Aligned_cols=71 Identities=17% Similarity=0.193 Sum_probs=58.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHHH
Q 011515 39 VVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTWQ 110 (484)
Q Consensus 39 AvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa 110 (484)
++..|.+-|.+.++..|..|..+|-.++.+|++. ...|.+...+..|+++++...+..||+.....|..-+
T Consensus 190 aVp~LV~LLsS~d~~lQ~eAa~aLa~Lass~ee~-~~aVIeaGaVP~LV~LL~sg~~~~VRE~AA~AL~nLA 260 (2102)
T PLN03200 190 GVDILVKLLSSGNSDAQANAASLLARLMMAFESS-ISKVLDAGAVKQLLKLLGQGNEVSVRAEAAGALEALS 260 (2102)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHcCChHH-HHHHHHCCCHHHHHHHHccCCChHHHHHHHHHHHHHh
Confidence 6778888899999999999999999999998764 4456677889999999987677789998887774433
No 94
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (DDs) are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=27.05 E-value=1.5e+02 Score=23.44 Aligned_cols=34 Identities=24% Similarity=0.333 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHhcC
Q 011515 98 VKEKILILIDTWQEAFGGPRARYPQYYAAYQELLRAGA 135 (484)
Q Consensus 98 VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~kGi 135 (484)
+.+++.+||..|....+. -..+...+..|++-|.
T Consensus 37 ~~~~~~~mL~~W~~~~~~----~at~~~L~~aL~~~~~ 70 (79)
T cd01670 37 VREQAYQLLLKWEEREGD----NATVGNLIEALREIGR 70 (79)
T ss_pred HHHHHHHHHHHHHhccCc----CcHHHHHHHHHHHcCH
Confidence 899999999999998864 2456677777877654
No 95
>PF12755 Vac14_Fab1_bd: Vacuolar 14 Fab1-binding region
Probab=26.84 E-value=3.9e+02 Score=22.94 Aligned_cols=64 Identities=17% Similarity=0.291 Sum_probs=46.5
Q ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHH
Q 011515 36 AKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKI 102 (484)
Q Consensus 36 akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKi 102 (484)
-++-++-|-+-+...+.+|-+.|.+-|-.++|.++..+-..+ .+..+.|.|++.. ++..||.-+
T Consensus 25 l~~Il~pVL~~~~D~d~rVRy~AcEaL~ni~k~~~~~~l~~f--~~IF~~L~kl~~D-~d~~Vr~~a 88 (97)
T PF12755_consen 25 LDEILPPVLKCFDDQDSRVRYYACEALYNISKVARGEILPYF--NEIFDALCKLSAD-PDENVRSAA 88 (97)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHcC-CchhHHHHH
Confidence 355666666777889999999999999999999987654322 3455556666654 577788755
No 96
>PF11864 DUF3384: Domain of unknown function (DUF3384); InterPro: IPR024584 This entry represents the N-terminal domain of tuberin which is functionally uncharacterised.
Probab=26.04 E-value=4.4e+02 Score=28.71 Aligned_cols=93 Identities=18% Similarity=0.235 Sum_probs=55.5
Q ss_pred HHHHHHHHHHHhCCCCCHHHH-HHHHHHHhCCC-CHHHHHHHHHHHHHHHhcccc-------hhhhhhcch-------HH
Q 011515 19 WAMNIEICDMLNHDPGQAKDV-VKGIKKRIGSR-NSKVQLLALTLLETIIKNCGD-------IVHMHVAEK-------NV 82 (484)
Q Consensus 19 w~~ileICD~In~~~~~akeA-vraIrKRL~s~-np~vqllAL~LLE~cVKNCG~-------~Fh~eVask-------~F 82 (484)
...+.++|+.|..-+-.+-++ ..+.+--|... .......++.||.+|++-.+. .|...|... .+
T Consensus 8 ~~a~~~l~~~i~~~~~~~i~~iW~~~~DLi~~~~p~e~R~~~~~ll~~~i~~~~~~~~~~R~~fF~~I~~~~~~~d~~~~ 87 (464)
T PF11864_consen 8 IKAAEELCESIQKYPLSSIEEIWYAAKDLIDPNQPSEARRAALELLIACIKRQDSSSGLMRAEFFRDISDPSNDDDFDLR 87 (464)
T ss_pred HHHHHHHHHHHHhCCchHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHhcCCCchhHHHH
Confidence 356788999999877665444 44444444444 455777889999999998866 333344321 34
Q ss_pred HHHHHHHhccCCCh-hHHHHHHHHHHHHHH
Q 011515 83 LHEMVKIARKKPDT-HVKEKILILIDTWQE 111 (484)
Q Consensus 83 LneLvkLv~~k~d~-~VkeKiLeLIq~Wa~ 111 (484)
++-|+.|-+...+. ..-..+..++-.|-.
T Consensus 88 l~aL~~LT~~Grdi~~~~~~i~~~L~~wl~ 117 (464)
T PF11864_consen 88 LEALIALTDNGRDIDFFEYEIGPFLLSWLE 117 (464)
T ss_pred HHHHHHHHcCCcCchhcccchHHHHHHHHH
Confidence 44444454443332 234455556666654
No 97
>PF09324 DUF1981: Domain of unknown function (DUF1981); InterPro: IPR015403 This domain is functionally uncharacterised and found in various plant and yeast protein transport proteins. It is noramlly associated with and C-termianl to the SEC7 domain. The SEC7 domain was named after the first protein found to contain such a region []. It has been shown to be linked with guanine nucleotide exchange function [, ].
Probab=25.92 E-value=1.7e+02 Score=24.41 Aligned_cols=36 Identities=28% Similarity=0.332 Sum_probs=28.6
Q ss_pred chHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHhC
Q 011515 79 EKNVLHEMVKIARKKPDTHVKEKILILIDTWQEAFG 114 (484)
Q Consensus 79 sk~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~aF~ 114 (484)
.++||.=+..++...++.+||+++++.|..--...+
T Consensus 15 Q~~fL~Pf~~i~~~~~~~~vre~il~ci~qil~~~~ 50 (86)
T PF09324_consen 15 QKDFLKPFEYIMSNNPSIDVRELILECILQILQSRG 50 (86)
T ss_pred HHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHHhH
Confidence 367888888888777889999999998877766543
No 98
>KOG3811 consensus Transcription factor AP-2 [Transcription]
Probab=25.76 E-value=1.3e+02 Score=32.78 Aligned_cols=55 Identities=22% Similarity=0.248 Sum_probs=24.9
Q ss_pred CCCCCCCCCCc--ccccccCCCCCCcccCCCCCCCCCCCCcccccccccCCCCCCCCCcCCCC
Q 011515 406 NMAGQPNSLAP--QFHQQQNFQTPEAGLYQNGTAPNMGSPRYEQSIYAQGSGPAWNGQLALPQ 466 (484)
Q Consensus 406 ~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 466 (484)
+.++++.+-.+ .|+..+.++++. +.||...+.. -|.+.. +...|-.||++.|+++
T Consensus 39 ~s~~p~~~~~~~~~~qP~~~f~p~y---~~~~~~~~~~--~y~~~~-~~~~~~~~~~l~aqP~ 95 (434)
T KOG3811|consen 39 YSSAPPFSHSGVSPFQPPYYFPPPY---QENGYSQSAD--PYSHPN-MDPYGIPLNPLHAQPL 95 (434)
T ss_pred CCCCCCCCCCCCCCcCCCCCCCCcc---cccccccccc--hhhcCC-CCccCCCCCccccCCC
Confidence 33455555555 455444344433 4555222211 233321 2233346887777653
No 99
>PF04961 FTCD_C: Formiminotransferase-cyclodeaminase; InterPro: IPR007044 Enzymes containing the cyclodeaminase domain function in channeling one-carbon units to the folate pool. In most cases, this domain catalyses the cyclisation of formimidoyltetrahydrofolate to methenyltetrahydrofolate as shown in reaction (1). In the methylotrophic bacterium Methylobacterium extorquens, however, it catalyses the interconversion of formyltetrahydrofolate and methylenetetrahydrofolate [],as shown in reaction (2) (1) 5-formimidoyltetrahydrofolate = 5,10-methenyltetrahydrofolate + NH(3) (2) 10- formyltetrahydrofolate = 5,10-methenyltetrahydrofolate + H(2)O In prokaryotes, this domain mostly occurs on its own, while in eukaryotes it is fused to a glutamate formiminotransferase domain (which catalyses the previous step in the pathway) to form the bifunctional enzyme formiminotransferase-cyclodeaminase []. The eukaryotic enzyme is a circular tetramer of homodimers [], while the prokaryotic enzyme is a dimer [, ]. The crystal structure of the cyclodeaminase enzyme (Q9X1P6 from SWISSPROT) from Thermaotogoa maritima has been studied []. It is a homodimer, where each monomer is composed of six alpha helices arranged in an up and down helical bundle, forming a novel fold. The location of the active site is not known, but sequence alignments revealed two clusters of conserved residues located in a deep pocket within the dimmer interface. This pocket was large enough to accommodate the reaction product and it was postulated that this is the active site.; GO: 0003824 catalytic activity, 0044237 cellular metabolic process; PDB: 2PFD_C 1O5H_B.
Probab=25.12 E-value=1.8e+02 Score=27.86 Aligned_cols=43 Identities=14% Similarity=0.326 Sum_probs=32.9
Q ss_pred HHHHHHHhhcCCCCCc-cCchHHHHHHHHHHHHHHHHHHHHhhc
Q 011515 197 DVLAEMLNALDPNNKE-GLRQEVIVDLVDQCRTYKQRVVHLVNS 239 (484)
Q Consensus 197 ~LL~EML~~~~P~~~e-~~d~Eli~EL~~~Cr~~q~rV~rLI~~ 239 (484)
--|..|..++.-+++. ..-.+.++++.++|..+|.+++.|+.+
T Consensus 31 aaL~~Mv~~lT~gkk~~~~~~~~~~~~~~~~~~~~~~ll~l~d~ 74 (184)
T PF04961_consen 31 AALGSMVANLTLGKKKYEDVEEELKEIIEKLEELREELLDLADE 74 (184)
T ss_dssp HHHHHHHHHCTTTSTTSGGGHHHHHHHHHHHHHHHHHHHCHHHH
T ss_pred HHHHHHHHHHhCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3466788888776543 234568899999999999999999853
No 100
>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=25.02 E-value=3.2e+02 Score=23.69 Aligned_cols=44 Identities=16% Similarity=0.342 Sum_probs=29.0
Q ss_pred hhhhhcchHHHHHHHHHhccCCC----------hhHHHHHHHHHHHHHHHhCCC
Q 011515 73 VHMHVAEKNVLHEMVKIARKKPD----------THVKEKILILIDTWQEAFGGP 116 (484)
Q Consensus 73 Fh~eVask~FLneLvkLv~~k~d----------~~VkeKiLeLIq~Wa~aF~~~ 116 (484)
++.-+...++++.|.......++ ..++.||+.+|..|-+.+..+
T Consensus 36 yr~F~tp~~ll~~L~~rf~~~~~~~~~~~~~~~~~~~~rv~~~l~~Wv~~~~~d 89 (127)
T smart00229 36 YRSFITTQELLQLLLYRYNAIPPESWVERKVNPLRVKNRVLNILRHWVENYWQD 89 (127)
T ss_pred hhhhCCHHHHHHHHHHHhCCCCcHHHHHHHhhHHHHHHHHHHHHHHHHHHCCcc
Confidence 33334456666666655443211 358999999999999998753
No 101
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=24.91 E-value=1.6e+02 Score=30.58 Aligned_cols=26 Identities=19% Similarity=0.509 Sum_probs=21.8
Q ss_pred hccCCChhHHHHHHHHHHHHHHHhCC
Q 011515 90 ARKKPDTHVKEKILILIDTWQEAFGG 115 (484)
Q Consensus 90 v~~k~d~~VkeKiLeLIq~Wa~aF~~ 115 (484)
+.++++.+|+..+.+||..|...+..
T Consensus 52 lrkh~~~~I~~lAk~li~~WK~~v~~ 77 (299)
T TIGR01385 52 LRKHPNEDISKLAKKIIKSWKKVVDK 77 (299)
T ss_pred HHcCCcHHHHHHHHHHHHHHHHHHhh
Confidence 34467889999999999999998853
No 102
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=24.72 E-value=1.9e+02 Score=24.20 Aligned_cols=69 Identities=13% Similarity=0.183 Sum_probs=41.6
Q ss_pred HHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHhcC
Q 011515 62 LETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTWQEAFGGPRARYPQYYAAYQELLRAGA 135 (484)
Q Consensus 62 LE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~kGi 135 (484)
++.+.+|-|..+..-.-.=.|-+.=+.-++... ..+++++..||..|.+..+.. .-+..+.+.|++-|.
T Consensus 10 l~~ia~~iG~~Wk~Lar~LGls~~dI~~i~~~~-~~~~eq~~~mL~~W~~r~g~~----AT~~~L~~aL~~~~~ 78 (86)
T cd08318 10 ITVFANKLGEDWKTLAPHLEMKDKEIRAIESDS-EDIKMQAKQLLVAWQDREGSQ----ATPETLITALNAAGL 78 (86)
T ss_pred HHHHHHHHhhhHHHHHHHcCCCHHHHHHHHhcC-CCHHHHHHHHHHHHHHhcCcc----ccHHHHHHHHHHcCc
Confidence 344556777766654333344433333343322 358999999999999987642 335566677776553
No 103
>PF14663 RasGEF_N_2: Rapamycin-insensitive companion of mTOR RasGEF_N domain
Probab=24.18 E-value=1.8e+02 Score=25.59 Aligned_cols=76 Identities=14% Similarity=0.167 Sum_probs=45.9
Q ss_pred HHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHH--------HhccCCCh---hHHHHHHHH
Q 011515 37 KDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVK--------IARKKPDT---HVKEKILIL 105 (484)
Q Consensus 37 keAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvk--------Lv~~k~d~---~VkeKiLeL 105 (484)
+=+++.|.+.|...++.|...|+.+|+-+..-- .....-|.-+..++.|.+ +++..... .=..-|-..
T Consensus 7 ~w~i~lLv~QL~D~~~~V~~~A~~iL~e~c~~~-~~le~~v~~~p~l~~L~~~g~~Ll~~~lS~~~Gf~~L~~~~~v~~E 85 (115)
T PF14663_consen 7 DWGIELLVTQLYDPSPEVVAAALEILEEACEDK-EYLEYLVSLRPSLDHLGDIGSPLLLRFLSTPSGFRYLNEIGYVEKE 85 (115)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhch-hhHHHHHHcCcHHHHHHHcCHHHHHHHHcchHHHHHhcchhHHHHH
Confidence 457889999999999999999999986554433 333333444444444443 22211111 112346677
Q ss_pred HHHHHHHh
Q 011515 106 IDTWQEAF 113 (484)
Q Consensus 106 Iq~Wa~aF 113 (484)
++.|-..+
T Consensus 86 l~~W~~~~ 93 (115)
T PF14663_consen 86 LDKWFESF 93 (115)
T ss_pred HHHHHHcc
Confidence 88888765
No 104
>KOG4535 consensus HEAT and armadillo repeat-containing protein [General function prediction only]
Probab=23.89 E-value=66 Score=35.89 Aligned_cols=45 Identities=24% Similarity=0.409 Sum_probs=35.9
Q ss_pred HHHHHhCCCCC------HHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcc
Q 011515 25 ICDMLNHDPGQ------AKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNC 69 (484)
Q Consensus 25 ICD~In~~~~~------akeAvraIrKRL~s~np~vqllAL~LLE~cVKNC 69 (484)
++.+|...+-. -.+.+..|||.|+|+++.|..-+|+||+++|...
T Consensus 131 la~lv~~~p~~~l~~~~~~~~~~~ik~~i~~~d~~v~vs~l~~~~~~v~t~ 181 (728)
T KOG4535|consen 131 LANLVSNAPYDRLKLSLLTKVWNQIKPYIRHKDVNVRVSSLTLLGAIVSTH 181 (728)
T ss_pred HHHHHhcCchHHHHHHHHHHHHHHHHHHhhcCCCChhhHHHHHHHHHHhcC
Confidence 45556555521 3578889999999999999999999999999753
No 105
>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=23.54 E-value=3.5e+02 Score=22.92 Aligned_cols=45 Identities=13% Similarity=0.335 Sum_probs=31.9
Q ss_pred hhhhhhcchHHHHHHHHHhccCC-------------ChhHHHHHHHHHHHHHHHhCCC
Q 011515 72 IVHMHVAEKNVLHEMVKIARKKP-------------DTHVKEKILILIDTWQEAFGGP 116 (484)
Q Consensus 72 ~Fh~eVask~FLneLvkLv~~k~-------------d~~VkeKiLeLIq~Wa~aF~~~ 116 (484)
.++.-+...++++.|+....... ...+|.+|+.+|..|-+.+..+
T Consensus 27 TyrsF~s~~~ll~~L~~rf~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~Wv~~~~~d 84 (122)
T cd06224 27 TYRSFTTPTELLEKLIERYEIAPPENLEYNDWDKKKSKPIRLRVLNVLRTWVENYPYD 84 (122)
T ss_pred HhhhhCCHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHhCCCc
Confidence 34444556777777777665321 2358999999999999998764
No 106
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=23.05 E-value=1.8e+02 Score=24.38 Aligned_cols=67 Identities=16% Similarity=0.157 Sum_probs=41.1
Q ss_pred HHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHH
Q 011515 62 LETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTWQEAFGGPRARYPQYYAAYQELLR 132 (484)
Q Consensus 62 LE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~ 132 (484)
|+.+.+|-|..+..-.-.=.|-+.=+..++...+..+++.+..||..|....+.. ..+..++..|++
T Consensus 7 l~~ia~~LG~dWk~LAr~Lg~se~dI~~i~~~~~~~~~eq~~~mL~~W~~r~g~~----At~~~L~~aL~~ 73 (84)
T cd08804 7 LAVIADHLGFSWTELARELDFTEEQIHQIRIENPNSLQDQSHALLKYWLERDGKH----ATDTNLMKCLTK 73 (84)
T ss_pred HHHHHHHHhhhHHHHHHHcCCCHHHHHHHHHHCcccHHHHHHHHHHHHHHccCCC----chHHHHHHHHHH
Confidence 4445577777766443444454444444444334569999999999999987532 234445555654
No 107
>PRK14148 heat shock protein GrpE; Provisional
Probab=22.86 E-value=3.6e+02 Score=26.37 Aligned_cols=66 Identities=12% Similarity=0.219 Sum_probs=46.0
Q ss_pred HHHHHHHHHHHHHHHHhhcCCCCCccCchHHHHHHHHHHHHHHHHHHHHhhcc---CCHHHHHHHhhhhHHHHHHHHH
Q 011515 188 EIQNARGIMDVLAEMLNALDPNNKEGLRQEVIVDLVDQCRTYKQRVVHLVNST---ADESLLCQGLQLNDDLQRLLAK 262 (484)
Q Consensus 188 eLe~ak~nv~LL~EML~~~~P~~~e~~d~Eli~EL~~~Cr~~q~rV~rLI~~~---~DEelL~eLL~aNDeL~~vL~r 262 (484)
+++.++..+.-|.+-+..+ .+.+.-+...+..+|+|..+=+... .-+.++.+||.+=|+|.++|..
T Consensus 41 e~~~l~~~l~~l~~e~~el---------kd~~lR~~Ae~eN~rKR~~rE~e~~~~~a~~~~~~~LLpV~DnlerAl~~ 109 (195)
T PRK14148 41 QLERAKDTIKELEDSCDQF---------KDEALRAKAEMENIRKRAERDVSNARKFGIEKFAKELLPVIDSIEQALKH 109 (195)
T ss_pred HHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHhHHHHHHhc
Confidence 4455554444444444333 2334567788888899988877654 5789999999999999999963
No 108
>PF12830 Nipped-B_C: Sister chromatid cohesion C-terminus
Probab=22.46 E-value=3.7e+02 Score=25.52 Aligned_cols=65 Identities=22% Similarity=0.390 Sum_probs=51.0
Q ss_pred HHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHhC
Q 011515 43 IKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTWQEAFG 114 (484)
Q Consensus 43 IrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~aF~ 114 (484)
|.+-..+.+..+.+.|+.+|+.+++.+ -.| =...+-.|+.|... ++..|+.++..++..-.+.+.
T Consensus 13 Il~~~~~~~~~vr~~Al~~l~~il~qG--Lvn----P~~cvp~lIAL~ts-~~~~ir~~A~~~l~~l~eK~~ 77 (187)
T PF12830_consen 13 ILELCLSSDDSVRLAALQVLELILRQG--LVN----PKQCVPTLIALETS-PNPSIRSRAYQLLKELHEKHE 77 (187)
T ss_pred HHHHHhCCCHHHHHHHHHHHHHHHhcC--CCC----hHHHHhHhhhhhCC-CChHHHHHHHHHHHHHHHHhH
Confidence 334446899999999999999999976 233 35567778887776 688999999999998887664
No 109
>PRK14140 heat shock protein GrpE; Provisional
Probab=22.45 E-value=3.9e+02 Score=26.04 Aligned_cols=44 Identities=23% Similarity=0.295 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhcc---CCHHHHHHHhhhhHHHHHHHHH
Q 011515 219 IVDLVDQCRTYKQRVVHLVNST---ADESLLCQGLQLNDDLQRLLAK 262 (484)
Q Consensus 219 i~EL~~~Cr~~q~rV~rLI~~~---~DEelL~eLL~aNDeL~~vL~r 262 (484)
+..+...+..+|+|..+=+... .-+.++.+||.+-|+|-++|..
T Consensus 60 ~lR~~Ae~eN~rkR~~rE~~~~~~~a~~~~~~~LLpvlDnLerAl~~ 106 (191)
T PRK14140 60 YLRLQADFENYKRRIQKENEAAEKYRAQSLASDLLPALDNFERALQI 106 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4456677888888888866654 5788999999999999999963
No 110
>PRK09458 pspB phage shock protein B; Provisional
Probab=21.87 E-value=1.1e+02 Score=25.65 Aligned_cols=25 Identities=16% Similarity=0.343 Sum_probs=20.5
Q ss_pred ccCchHHHHHHHHHHHHHHHHHHHH
Q 011515 212 EGLRQEVIVDLVDQCRTYKQRVVHL 236 (484)
Q Consensus 212 e~~d~Eli~EL~~~Cr~~q~rV~rL 236 (484)
+..|...+++|+++.++|+.||.-|
T Consensus 37 s~~d~~~L~~L~~~A~rm~~RI~tL 61 (75)
T PRK09458 37 SQEEQQRLAQLTEKAERMRERIQAL 61 (75)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3446678999999999999999764
No 111
>KOG1511 consensus Mevalonate kinase MVK/ERG12 [Lipid transport and metabolism]
Probab=21.67 E-value=1.9e+02 Score=31.01 Aligned_cols=44 Identities=25% Similarity=0.311 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhc----c--CCHHHHHHHhhhhHHHHHHH
Q 011515 217 EVIVDLVDQCRTYKQRVVHLVNS----T--ADESLLCQGLQLNDDLQRLL 260 (484)
Q Consensus 217 Eli~EL~~~Cr~~q~rV~rLI~~----~--~DEelL~eLL~aNDeL~~vL 260 (484)
|+|+.+++.|..+-.....+++. . .+|+-|.+|+.+|-+|..+|
T Consensus 259 evi~~i~~aid~is~ea~~il~~e~~~~~~~~Eq~L~eLi~iNq~LL~al 308 (397)
T KOG1511|consen 259 EVIKAIFDAIDEISLEAVWILQRENDEFSSPKEQKLEELIRINQDLLDAL 308 (397)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccccCCCcHHHHHHHHHHHhHHHHHHh
Confidence 57888888888888888888873 1 34667999999999988776
No 112
>KOG4508 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.66 E-value=2.6e+02 Score=30.50 Aligned_cols=95 Identities=16% Similarity=0.192 Sum_probs=53.6
Q ss_pred CHHHHHHHHHHHhCCC----------CHHHHHHHHHH--------------HHHHHhcccchhhhhhcchHHHHHHHHHh
Q 011515 35 QAKDVVKGIKKRIGSR----------NSKVQLLALTL--------------LETIIKNCGDIVHMHVAEKNVLHEMVKIA 90 (484)
Q Consensus 35 ~akeAvraIrKRL~s~----------np~vqllAL~L--------------LE~cVKNCG~~Fh~eVask~FLneLvkLv 90 (484)
+++-|+..|.|-..+. |-...+.++++ +..-+.|| -.|-.++-++-.-|++|+||
T Consensus 386 Np~~A~e~L~kl~~S~qi~~Y~~~l~nmdmslHSmEvVnrLttav~lp~~fi~~yi~nc-is~ce~~kdkymqnRlVRLV 464 (522)
T KOG4508|consen 386 NPKFAGEFLVKLALSEQIKRYMRLLENMDMSLHSMEVVNRLTTAVILPDKFIQEYIENC-ISFCEHTKDKYMQNRLVRLV 464 (522)
T ss_pred ChHHHHHHHHHHhhHHHHHHHHHHHhcccchhHHHHHHHHHhhhhcCCHHHHHHHHHHH-HHHHHHHHHHHhhhhhHHHH
Confidence 5688888877766553 33333344433 23345577 34555555666667788877
Q ss_pred ccCCChhHHHHHHHHH------HHHHHHhCCCCCCchHHHHHHHHHHHhc
Q 011515 91 RKKPDTHVKEKILILI------DTWQEAFGGPRARYPQYYAAYQELLRAG 134 (484)
Q Consensus 91 ~~k~d~~VkeKiLeLI------q~Wa~aF~~~~~~~~~i~~~Y~~Lk~kG 134 (484)
.--...-+|+||+.+= +.+...|.+ ......+|+.||.-|
T Consensus 465 cvflqsLiRnkIiNV~DlfieVqaFciefsr----~REaagLfrllkqld 510 (522)
T KOG4508|consen 465 CVFLQSLIRNKIINVEDLFIEVQAFCIEFSR----NREAAGLFRLLKQLD 510 (522)
T ss_pred HHHHHHHHHHhcccHHHHHHHHHhhhhhhhh----hHHHHHHHHHHHHhc
Confidence 5422335666666553 444444432 344567889888743
No 113
>PF09712 PHA_synth_III_E: Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E)
Probab=21.45 E-value=1.6e+02 Score=30.47 Aligned_cols=91 Identities=5% Similarity=0.123 Sum_probs=64.9
Q ss_pred HHHHHHHHHHHhCC-CCHHHHHHHH-HHHHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHh
Q 011515 36 AKDVVKGIKKRIGS-RNSKVQLLAL-TLLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTWQEAF 113 (484)
Q Consensus 36 akeAvraIrKRL~s-~np~vqllAL-~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~aF 113 (484)
...++..+.+||.. .....+.-+. .+-|.=|+.|...|-..+++.+|..-+.+++.. -..+|...=+++..|-..+
T Consensus 189 ~~~a~~~~~~~l~~~~~~g~~~~s~re~~d~Wi~~ae~~~~~~~~S~ef~~~~g~~~~a--~m~~r~~~~~~~e~~L~~l 266 (293)
T PF09712_consen 189 WMKAFERMMEKLQERAEEGEQIKSWREFYDIWIDAAEEAYEELFRSEEFAQAYGQLVNA--LMDLRKQQQEVVEEYLRSL 266 (293)
T ss_pred HHHHHHHHHHHHHHhhccCCCCcCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHC
Confidence 46677777777732 1111222233 567888999999999999999999999999985 3578999999999999887
Q ss_pred CCCCCCchHHHHHHHHH
Q 011515 114 GGPRARYPQYYAAYQEL 130 (484)
Q Consensus 114 ~~~~~~~~~i~~~Y~~L 130 (484)
.-.. -..|-++|+.|
T Consensus 267 ~lPT--r~evd~l~k~l 281 (293)
T PF09712_consen 267 NLPT--RSEVDELYKRL 281 (293)
T ss_pred CCCC--HHHHHHHHHHH
Confidence 6321 23455666554
No 114
>PRK14162 heat shock protein GrpE; Provisional
Probab=21.10 E-value=4e+02 Score=26.04 Aligned_cols=45 Identities=20% Similarity=0.158 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcc---CCHHHHHHHhhhhHHHHHHHHH
Q 011515 218 VIVDLVDQCRTYKQRVVHLVNST---ADESLLCQGLQLNDDLQRLLAK 262 (484)
Q Consensus 218 li~EL~~~Cr~~q~rV~rLI~~~---~DEelL~eLL~aNDeL~~vL~r 262 (484)
.+..+...+..+|+|..+-+... .-+.++.+||.+=|+|.+||..
T Consensus 61 ~~lR~~AEfeN~rkR~~kE~e~~~~~a~~~~~~~LLpV~DnLerAl~~ 108 (194)
T PRK14162 61 KYLRSQAEIQNMQNRYAKERAQLIKYESQSLAKDVLPAMDNLERALAV 108 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHhHHHHHHhc
Confidence 34567777888888988876654 5788999999999999999963
No 115
>PF10363 DUF2435: Protein of unknown function (DUF2435)
Probab=21.02 E-value=4.3e+02 Score=22.48 Aligned_cols=68 Identities=9% Similarity=0.074 Sum_probs=41.1
Q ss_pred HHHHHHHcCCCCCCcCHHHHHHHHHHHhCCC---CCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccc
Q 011515 3 NSMVDRATSDMLIGPDWAMNIEICDMLNHDP---GQAKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGD 71 (484)
Q Consensus 3 ~~lIekATse~l~~~Dw~~ileICD~In~~~---~~akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~ 71 (484)
.++++..+++..+---++ ...+..+|.+.. ....-.+..+..-|++.++-+=+.|+..|.+|..-.+.
T Consensus 6 ~~al~~L~dp~~PvRa~g-L~~L~~Li~~~~~~~~~~~~il~l~l~~L~d~DsyVYL~aI~~L~~La~~~p~ 76 (92)
T PF10363_consen 6 QEALSDLNDPLPPVRAHG-LVLLRKLIESKSEPVIDIPKILDLFLSQLKDEDSYVYLNAIKGLAALADRHPD 76 (92)
T ss_pred HHHHHHccCCCcchHHHH-HHHHHHHHHcCCcchhhHHHHHHHHHHHcCCCCchHHHHHHHHHHHHHHHChH
Confidence 345555566555444444 344777777655 23344555666667777777777777777777655543
No 116
>COG5369 Uncharacterized conserved protein [Function unknown]
Probab=20.97 E-value=2.6e+02 Score=31.86 Aligned_cols=89 Identities=15% Similarity=0.272 Sum_probs=59.7
Q ss_pred HHHHHHHHhC-CCCC----HHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhcccchhhhhhcchHHHHHHHHHhccCCCh
Q 011515 22 NIEICDMLNH-DPGQ----AKDVVKGIKKRIGSRNSKVQLLALTLLETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDT 96 (484)
Q Consensus 22 ileICD~In~-~~~~----akeAvraIrKRL~s~np~vqllAL~LLE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~ 96 (484)
-..||+.|-. ++-+ -+-.+..|.+-+.+++...|-.++-+|.-+|-||.+..+.++-.|-=++.++..+ +.+.-
T Consensus 452 t~~icn~vv~fsnL~~~fL~~~iIdvl~~~v~sKDdaLqans~wvlrHlmyncq~~ekf~~Lakig~~kvl~~~-NDpc~ 530 (743)
T COG5369 452 TIDICNKVVPFSNLGAGFLEKSIIDVLVNLVMSKDDALQANSEWVLRHLMYNCQKNEKFKFLAKIGVEKVLSYT-NDPCF 530 (743)
T ss_pred hhhhhheeeeccchHHHHHHhhHHHHHHHHhhcchhhhhhcchhhhhhhhhcCcchhhhhhHHhcCHHHHHHHh-cCccc
Confidence 4567877543 3322 3567778888888999888888899999999999876554333332233333333 23566
Q ss_pred hHHHHHHHHHHHHHH
Q 011515 97 HVKEKILILIDTWQE 111 (484)
Q Consensus 97 ~VkeKiLeLIq~Wa~ 111 (484)
.|++.++.++..+.-
T Consensus 531 ~vq~q~lQilrNftc 545 (743)
T COG5369 531 KVQHQVLQILRNFTC 545 (743)
T ss_pred ccHHHHHHHHHhccc
Confidence 888888888877653
No 117
>PRK14154 heat shock protein GrpE; Provisional
Probab=20.79 E-value=3.6e+02 Score=26.75 Aligned_cols=44 Identities=14% Similarity=0.174 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhcc---CCHHHHHHHhhhhHHHHHHHHH
Q 011515 219 IVDLVDQCRTYKQRVVHLVNST---ADESLLCQGLQLNDDLQRLLAK 262 (484)
Q Consensus 219 i~EL~~~Cr~~q~rV~rLI~~~---~DEelL~eLL~aNDeL~~vL~r 262 (484)
+.-+...+..+|+|..+-++.. .-+.++..||.+=|+|.++|..
T Consensus 75 ~lRl~ADfeNyRKR~~kE~e~~~~~a~e~~~~~LLpVlDnLeRAL~~ 121 (208)
T PRK14154 75 YLRAQAEMDNLRKRIEREKADIIKFGSKQLITDLLPVADSLIHGLES 121 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHhHHHHHHhc
Confidence 3467777888888888877654 5788999999999999999874
No 118
>PF11083 Streptin-Immun: Lantibiotic streptin immunity protein; InterPro: IPR021112 Streptococcal species produce a lantibiotic, streptin, in a similar manner to the production of nisin and subtilin by other lactic acid bacteria, in order to compete against competing bacteria within the environment []. The immunity protein protects the bacterium from destruction by its own lantibiotic. In general, there is little homology between the immunity proteins of different genera of bacteria.
Probab=20.73 E-value=4.9e+02 Score=22.94 Aligned_cols=31 Identities=19% Similarity=0.118 Sum_probs=26.3
Q ss_pred ccCCHHHHHHHhhhhHHHHHHHHHHHhhhcC
Q 011515 239 STADESLLCQGLQLNDDLQRLLAKHESFASG 269 (484)
Q Consensus 239 ~~~DEelL~eLL~aNDeL~~vL~rYe~l~~g 269 (484)
.+.=|.+-.++..+..+|..-+.+||.+++.
T Consensus 51 sitle~ve~Ei~~lQ~qL~~~ldeYE~~Vrr 81 (99)
T PF11083_consen 51 SITLEQVEKEIRELQNQLGLYLDEYEKLVRR 81 (99)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3466788889999999999999999998764
No 119
>PTZ00429 beta-adaptin; Provisional
Probab=20.72 E-value=6.5e+02 Score=29.59 Aligned_cols=35 Identities=17% Similarity=0.144 Sum_probs=27.2
Q ss_pred HHHhCCCCCHHHHHHHHHHHhCCCCHHHHHHHHHH
Q 011515 27 DMLNHDPGQAKDVVKGIKKRIGSRNSKVQLLALTL 61 (484)
Q Consensus 27 D~In~~~~~akeAvraIrKRL~s~np~vqllAL~L 61 (484)
.+.+.+++-+--|+..|+|-++++||.+.-+||..
T Consensus 94 ~ya~~~pelalLaINtl~KDl~d~Np~IRaLALRt 128 (746)
T PTZ00429 94 STARLQPEKALLAVNTFLQDTTNSSPVVRALAVRT 128 (746)
T ss_pred HHcccChHHHHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence 34444556677899999999999999998888853
No 120
>PF09758 FPL: Uncharacterised conserved protein; InterPro: IPR019155 The proteins in this family are functionally uncharacterised. They contain a highly conserved FPL motif.
Probab=20.12 E-value=2.6e+02 Score=26.24 Aligned_cols=48 Identities=19% Similarity=0.259 Sum_probs=40.7
Q ss_pred cchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHhCCCC
Q 011515 70 GDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTWQEAFGGPR 117 (484)
Q Consensus 70 G~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~aF~~~~ 117 (484)
...|...++++.++..++++++......|+-++|..+.-|=+..++..
T Consensus 15 ~~~~Fd~F~E~nil~~f~~il~~~~~~~V~~QlLQtlsiLiqNi~~~~ 62 (149)
T PF09758_consen 15 DPSFFDFFMEKNILSTFVRILKQSRSSSVKLQLLQTLSILIQNIRSET 62 (149)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHhcCCCc
Confidence 345778899999999999999887778999999999998888887643
No 121
>cd08803 Death_ank3 Death domain of Ankyrin-3. Death Domain (DD) of the human protein ankyrin-3 (ANK-3) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-3, also called anykyrin-G (for general or giant), is found in neurons and at least one splice variant has been shown to be essential for propagation of action potentials as a binding partner to neurofascin and voltage-gated sodium channels. It is required for maintaining axo-dendritic polarity, and may be a genetic risk factor associated with bipolar disorder. ANK-3 may also play roles in other cell types. Mutations affecting ANK-3 pathways for Na channel localization are associated with Brugada syndrome, a potentially fata arrythmia. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by se
Probab=20.11 E-value=2.7e+02 Score=23.45 Aligned_cols=69 Identities=13% Similarity=0.127 Sum_probs=43.6
Q ss_pred HHHHHhcccchhhhhhcchHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHhc
Q 011515 62 LETIIKNCGDIVHMHVAEKNVLHEMVKIARKKPDTHVKEKILILIDTWQEAFGGPRARYPQYYAAYQELLRAG 134 (484)
Q Consensus 62 LE~cVKNCG~~Fh~eVask~FLneLvkLv~~k~d~~VkeKiLeLIq~Wa~aF~~~~~~~~~i~~~Y~~Lk~kG 134 (484)
|..+..|-|.....-...=.|-..=+..++...+..+.+++..+|..|....+.. ..+..+...|++-|
T Consensus 7 l~~ia~~LG~dW~~LA~eLg~s~~dI~~i~~e~p~~~~~q~~~lL~~W~~r~g~~----At~~~L~~aL~~i~ 75 (84)
T cd08803 7 MAIVADHLGLSWTELARELNFSVDEINQIRVENPNSLIAQSFMLLKKWVTRDGKN----ATTDALTSVLTKIN 75 (84)
T ss_pred HHHHHHHhhccHHHHHHHcCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHHhhCCC----cHHHHHHHHHHHCC
Confidence 4445566677666444444444443344444444569999999999999987542 44556677777654
No 122
>PF08711 Med26: TFIIS helical bundle-like domain; InterPro: IPR017923 Transcription factor IIS (TFIIS) is a transcription elongation factor that increases the overall transcription rate of RNA polymerase II by reactivating transcription elongation complexes that have arrested transcription. The three structural domains of TFIIS are conserved from yeast to human. The 80 or so N-terminal residues form a protein interaction domain containing a conserved motif, which has been called the LW motif because of the invariant leucine and tryptophan residues it contains. Although the N-terminal domain is not needed for transcriptional activity, a similar sequence has been identified in other transcription factors and proteins that are predominantly nuclear localized [, ]: MED26 (also known as CRSP70 and ARC70), a subunit of the Mediator complex, which is required for the activity of the enhancer-binding protein Sp1. Elongin A, a subunit of a transcription elongation factor previously known as SIII. It increases the rate of transcription by suppressing transient pausing of the elongation complex. PPP1R10, a nuclear regulatory subunit of protein phosphatase 1 that was previously known as p99, FB19 or PNUTS. PIBP, a small hypothetical protein that could be a phosphoinositide binding protein. IWS1, which is thought to function in both transcription initiation and elongation. The TFIIS N-terminal domain is a compact four-helix bundle. The hydrophobic core residues of helices 2, 3, and 4 are well conserved among TFIIS domains, although helix 1 is less conserved []. ; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 1EO0_A 3OAK_A 3NFQ_B 3O8Z_A 1WJT_A 2XPL_A 2XPO_A 2XPP_A 2XPN_A.
Probab=20.06 E-value=1.9e+02 Score=21.64 Aligned_cols=20 Identities=15% Similarity=0.426 Sum_probs=17.0
Q ss_pred CChhHHHHHHHHHHHHHHHh
Q 011515 94 PDTHVKEKILILIDTWQEAF 113 (484)
Q Consensus 94 ~d~~VkeKiLeLIq~Wa~aF 113 (484)
.+++|++++.++|..|...+
T Consensus 33 ~~~~i~~~A~~Li~~Wk~~v 52 (53)
T PF08711_consen 33 ENPEIRKLAKELIKKWKRIV 52 (53)
T ss_dssp S-HHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHhHhc
Confidence 68899999999999998753
Done!