Query 032005
Match_columns 149
No_of_seqs 130 out of 680
Neff 8.3
Searched_HMMs 46136
Date Fri Mar 29 08:19:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032005.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032005hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00917 PG-PI_TP The phosphati 100.0 1.9E-31 4.2E-36 184.1 16.3 116 23-138 1-122 (122)
2 KOG4680 Uncharacterized conser 100.0 6.4E-30 1.4E-34 174.9 15.1 132 18-149 22-153 (153)
3 cd00918 Der-p2_like Several gr 100.0 4.1E-30 8.9E-35 176.6 12.1 117 23-140 1-120 (120)
4 cd00916 Npc2_like Niemann-Pick 100.0 6E-30 1.3E-34 176.8 12.7 116 23-138 1-123 (123)
5 smart00737 ML Domain involved 100.0 3.9E-29 8.5E-34 171.5 15.4 113 23-138 1-118 (118)
6 PF02221 E1_DerP2_DerF2: ML do 100.0 6.5E-29 1.4E-33 173.3 14.0 121 20-140 1-134 (134)
7 KOG4063 Major epididymal secre 100.0 1.8E-28 3.8E-33 170.4 13.0 128 15-142 19-158 (158)
8 cd00912 ML The ML (MD-2-relate 99.9 1.2E-26 2.7E-31 161.1 13.2 115 23-137 1-126 (127)
9 cd00915 MD-1_MD-2 MD-1 and MD- 99.9 1.2E-23 2.6E-28 145.3 12.9 112 20-138 10-130 (130)
10 cd00258 GM2-AP GM2 activator p 99.8 3.3E-19 7.1E-24 126.5 14.7 121 20-142 2-161 (162)
11 PF14558 TRP_N: ML-like domain 98.8 1.3E-07 2.8E-12 66.7 11.0 119 20-142 4-138 (141)
12 PF15418 DUF4625: Domain of un 97.6 0.0019 4.1E-08 45.1 11.0 104 35-140 16-131 (132)
13 smart00697 DM8 Repeats found i 96.7 0.012 2.6E-07 37.8 7.1 36 91-126 40-79 (93)
14 PF14524 Wzt_C: Wzt C-terminal 96.1 0.094 2E-06 35.8 9.2 89 33-124 12-108 (142)
15 PF07705 CARDB: CARDB; InterP 95.4 0.31 6.7E-06 31.2 9.0 81 33-124 3-84 (101)
16 PF06477 DUF1091: Protein of u 95.3 0.028 6E-07 35.4 3.5 29 91-119 49-81 (81)
17 PF02115 Rho_GDI: RHO protein 95.2 0.38 8.3E-06 35.9 9.8 94 46-142 103-199 (200)
18 PF10633 NPCBM_assoc: NPCBM-as 94.6 0.18 3.8E-06 31.5 5.9 72 47-124 2-76 (78)
19 PLN00044 multi-copper oxidase- 94.4 0.26 5.6E-06 42.6 8.3 17 90-106 102-119 (596)
20 PF04234 CopC: CopC domain; I 94.1 0.28 6E-06 32.1 6.3 35 103-137 60-95 (97)
21 PRK10301 hypothetical protein; 93.2 0.26 5.6E-06 33.9 5.1 29 103-131 87-115 (124)
22 smart00675 DM11 Domains in hyp 92.5 3 6.5E-05 30.2 10.4 105 20-128 10-161 (164)
23 PLN02991 oxidoreductase 91.5 0.9 1.9E-05 38.9 7.2 34 73-106 83-118 (543)
24 PF05404 TRAP-delta: Transloco 91.2 3 6.6E-05 30.2 8.7 102 1-127 1-104 (167)
25 PF00339 Arrestin_N: Arrestin 89.6 0.57 1.2E-05 32.1 3.8 32 92-123 87-126 (149)
26 PLN02168 copper ion binding / 88.0 2.7 5.8E-05 36.1 7.5 54 46-106 61-116 (545)
27 PLN02354 copper ion binding / 87.9 2.1 4.6E-05 36.7 6.8 17 90-106 100-117 (552)
28 KOG3205 Rho GDP-dissociation i 87.6 9.5 0.00021 28.2 10.1 92 46-142 101-197 (200)
29 PF03443 Glyco_hydro_61: Glyco 87.2 2.5 5.4E-05 31.9 6.1 40 102-141 136-183 (218)
30 TIGR02186 alph_Pro_TM conserve 86.5 3.3 7.2E-05 32.2 6.5 41 101-142 181-221 (261)
31 PF09608 Alph_Pro_TM: Putative 84.8 4.6 0.0001 30.9 6.6 41 101-142 156-196 (236)
32 cd00918 Der-p2_like Several gr 84.7 2.2 4.7E-05 29.2 4.3 34 43-76 72-105 (120)
33 cd00912 ML The ML (MD-2-relate 84.0 3.4 7.4E-05 28.1 5.1 40 84-123 15-55 (127)
34 PF13002 LDB19: Arrestin_N ter 83.8 4.8 0.0001 29.8 6.0 52 92-143 44-114 (191)
35 PF07495 Y_Y_Y: Y_Y_Y domain; 83.4 1.7 3.7E-05 25.7 3.1 29 112-140 36-65 (66)
36 smart00737 ML Domain involved 83.2 3 6.6E-05 27.8 4.6 33 43-75 71-103 (118)
37 PF02221 E1_DerP2_DerF2: ML do 82.8 2.4 5.3E-05 28.7 4.1 34 42-75 84-117 (134)
38 PF00868 Transglut_N: Transglu 82.2 6.9 0.00015 26.5 6.0 78 46-124 29-117 (118)
39 PLN02835 oxidoreductase 81.7 7.5 0.00016 33.3 7.3 34 73-106 84-119 (539)
40 PF12988 DUF3872: Domain of un 81.4 4.1 9E-05 28.5 4.7 100 22-129 17-125 (137)
41 KOG1263 Multicopper oxidases [ 81.1 4.5 9.6E-05 34.9 5.8 34 73-107 83-119 (563)
42 COG2372 CopC Uncharacterized p 80.7 6.8 0.00015 27.1 5.5 29 103-131 88-116 (127)
43 PF13956 Ibs_toxin: Toxin Ibs, 80.1 1.3 2.9E-05 19.9 1.2 13 1-13 1-13 (19)
44 cd00916 Npc2_like Niemann-Pick 79.8 4.2 9.1E-05 27.7 4.3 35 42-76 75-109 (123)
45 PF12984 DUF3868: Domain of un 79.3 10 0.00023 25.6 6.1 31 33-67 29-60 (115)
46 COG2967 ApaG Uncharacterized p 77.2 4.8 0.0001 27.6 3.8 35 95-131 75-110 (126)
47 PRK05461 apaG CO2+/MG2+ efflux 77.1 8.9 0.00019 26.5 5.3 49 92-142 72-122 (127)
48 PF01835 A2M_N: MG2 domain; I 75.9 18 0.00038 23.1 6.5 72 47-126 12-88 (99)
49 PLN02604 oxidoreductase 75.7 14 0.00031 31.8 7.3 16 91-106 100-116 (566)
50 PF13752 DUF4165: Domain of un 75.6 21 0.00046 24.6 6.7 44 98-142 78-121 (124)
51 COG1470 Predicted membrane pro 75.1 42 0.0009 28.5 9.4 32 95-126 438-470 (513)
52 PF15432 Sec-ASP3: Accessory S 74.6 11 0.00025 26.0 5.3 37 92-131 46-84 (128)
53 PLN02792 oxidoreductase 74.6 6.3 0.00014 33.8 4.8 54 46-106 51-106 (536)
54 PF13754 Big_3_4: Bacterial Ig 74.1 11 0.00023 21.8 4.4 34 107-141 17-50 (54)
55 PF09551 Spore_II_R: Stage II 71.4 5.3 0.00012 27.8 3.0 26 112-137 93-119 (130)
56 PF07732 Cu-oxidase_3: Multico 71.3 4.6 0.0001 27.3 2.7 61 46-117 30-93 (117)
57 PF06775 Seipin: Putative adip 71.0 19 0.0004 26.6 6.1 44 95-138 53-100 (199)
58 PF03067 Chitin_bind_3: Chitin 68.7 32 0.00069 24.8 6.9 88 47-137 82-183 (183)
59 KOG3780 Thioredoxin binding pr 67.7 9.4 0.0002 31.2 4.3 31 95-125 102-140 (427)
60 TIGR01480 copper_res_A copper- 66.2 12 0.00026 32.5 4.8 16 91-106 118-134 (587)
61 TIGR02837 spore_II_R stage II 63.8 8.8 0.00019 27.8 3.0 26 112-137 128-154 (168)
62 PF15240 Pro-rich: Proline-ric 63.5 4.5 9.7E-05 29.7 1.5 15 5-19 3-17 (179)
63 cd00917 PG-PI_TP The phosphati 62.7 25 0.00054 23.7 5.0 32 91-122 20-53 (122)
64 PRK12633 flgD flagellar basal 61.1 15 0.00032 28.0 4.0 37 95-131 151-189 (230)
65 PRK12634 flgD flagellar basal 60.8 16 0.00035 27.6 4.1 36 95-130 144-181 (221)
66 KOG4063 Major epididymal secre 60.7 20 0.00044 25.6 4.3 33 44-76 108-140 (158)
67 PF11797 DUF3324: Protein of u 60.5 41 0.00088 23.3 5.9 45 95-142 86-131 (140)
68 PF12690 BsuPI: Intracellular 59.4 13 0.00028 23.5 3.0 26 95-121 56-82 (82)
69 PF02494 HYR: HYR domain; Int 59.1 16 0.00034 22.6 3.3 25 110-134 52-76 (81)
70 TIGR03711 acc_sec_asp3 accesso 58.7 23 0.00049 24.8 4.2 40 91-131 56-95 (135)
71 PRK10350 hypothetical protein; 58.3 4.6 0.0001 27.9 0.7 26 1-27 1-26 (145)
72 PF13750 Big_3_3: Bacterial Ig 55.5 59 0.0013 23.1 6.1 47 96-143 104-150 (158)
73 TIGR03389 laccase laccase, pla 53.1 52 0.0011 28.2 6.4 16 91-106 78-94 (539)
74 PF04729 ASF1_hist_chap: ASF1 52.8 38 0.00081 24.3 4.6 77 33-114 3-86 (154)
75 PRK12812 flgD flagellar basal 51.9 26 0.00056 27.3 4.0 21 111-131 181-201 (259)
76 PF04379 DUF525: Protein of un 50.8 25 0.00054 22.7 3.2 34 92-127 55-90 (90)
77 cd00915 MD-1_MD-2 MD-1 and MD- 49.4 28 0.00061 24.2 3.5 33 42-75 81-115 (130)
78 PF11141 DUF2914: Protein of u 48.4 59 0.0013 19.6 6.0 42 94-139 24-66 (66)
79 TIGR03390 ascorbOXfungal L-asc 46.3 41 0.0009 28.8 4.8 16 91-106 84-100 (538)
80 PF08737 Rgp1: Rgp1; InterPro 44.0 91 0.002 25.9 6.3 49 94-142 114-173 (415)
81 PF10029 DUF2271: Predicted pe 43.8 93 0.002 21.7 5.5 44 95-140 74-120 (139)
82 PF13860 FlgD_ig: FlgD Ig-like 43.4 21 0.00045 22.2 2.0 32 95-126 47-80 (81)
83 PF14734 DUF4469: Domain of un 41.6 45 0.00099 22.1 3.5 23 103-125 65-87 (102)
84 cd03451 FkbR2 FkbR2 is a Strep 40.6 1.1E+02 0.0025 20.6 6.2 45 93-137 90-139 (146)
85 TIGR03660 T1SS_rpt_143 T1SS-14 39.2 1.3E+02 0.0029 20.9 5.8 48 98-146 66-115 (137)
86 cd00146 PKD polycystic kidney 38.4 82 0.0018 18.9 4.2 18 113-130 55-72 (81)
87 PF07610 DUF1573: Protein of u 38.0 71 0.0015 17.5 4.2 34 22-58 3-45 (45)
88 PF11614 FixG_C: IG-like fold 36.7 1.2E+02 0.0027 19.9 5.5 37 95-131 70-108 (118)
89 PF08139 LPAM_1: Prokaryotic m 36.4 15 0.00032 18.0 0.3 11 2-12 8-18 (25)
90 PRK06655 flgD flagellar basal 36.3 62 0.0013 24.6 3.9 13 112-124 167-179 (225)
91 PF10956 DUF2756: Protein of u 36.0 16 0.00035 24.2 0.6 24 1-25 1-24 (104)
92 PRK10965 multicopper oxidase; 35.0 62 0.0013 27.7 4.1 16 91-106 116-132 (523)
93 PF13473 Cupredoxin_1: Cupredo 34.9 31 0.00068 22.3 1.9 28 32-59 23-52 (104)
94 cd02859 AMPKbeta_GBD_like AMP- 34.4 1.1E+02 0.0025 18.7 4.4 12 67-78 13-24 (79)
95 KOG1903 Cell cycle-associated 33.7 14 0.00031 26.8 0.1 40 67-106 61-103 (217)
96 KOG4824 Apolipoprotein D/Lipoc 33.6 19 0.0004 27.0 0.7 29 1-29 8-36 (224)
97 PF00879 Defensin_propep: Defe 33.2 25 0.00054 20.4 1.0 26 3-28 2-27 (52)
98 PF00801 PKD: PKD domain; Int 32.5 57 0.0012 19.2 2.7 16 114-129 51-66 (69)
99 PF12245 Big_3_2: Bacterial Ig 32.0 83 0.0018 18.4 3.3 35 107-142 15-49 (60)
100 COG1952 SecB Preprotein transl 30.9 61 0.0013 23.3 2.9 27 69-95 76-106 (157)
101 PF10651 DUF2479: Domain of un 30.7 1.2E+02 0.0026 21.6 4.5 44 97-142 81-125 (170)
102 PLN02191 L-ascorbate oxidase 30.6 79 0.0017 27.4 4.1 16 91-106 99-115 (574)
103 PF03170 BcsB: Bacterial cellu 29.5 3.5E+02 0.0075 23.5 7.8 72 50-133 44-116 (605)
104 PF02495 7kD_coat: 7kD viral c 28.9 21 0.00046 21.0 0.3 7 20-26 21-27 (59)
105 PF02018 CBM_4_9: Carbohydrate 28.1 1.3E+02 0.0028 19.4 4.1 31 93-128 56-87 (131)
106 PRK15346 outer membrane secret 28.0 32 0.00068 29.2 1.2 25 1-25 1-28 (499)
107 PF11033 ComJ: Competence prot 27.8 1.2E+02 0.0027 20.9 3.9 15 91-105 90-104 (125)
108 cd03452 MaoC_C MaoC_C The C-t 27.5 2E+02 0.0044 19.5 6.3 48 92-139 86-137 (142)
109 PRK10883 FtsI repressor; Provi 27.4 1.1E+02 0.0025 25.7 4.4 17 89-105 114-131 (471)
110 PRK09619 flgD flagellar basal 27.3 1.1E+02 0.0024 23.1 3.9 15 111-125 159-173 (218)
111 PRK15098 beta-D-glucoside gluc 27.3 2.3E+02 0.0049 25.6 6.5 74 33-106 650-725 (765)
112 PRK15191 fimbrial protein BcfF 27.3 1.4E+02 0.0031 21.2 4.4 14 1-14 1-14 (172)
113 PLN03160 uncharacterized prote 26.9 2.8E+02 0.006 20.8 7.5 11 69-79 114-124 (219)
114 PF07760 DUF1616: Protein of u 26.8 3.1E+02 0.0067 21.4 12.3 93 41-137 182-282 (287)
115 COG3009 Uncharacterized protei 26.7 2.6E+02 0.0056 20.7 5.6 50 91-140 104-157 (190)
116 KOG4680 Uncharacterized conser 26.0 1.2E+02 0.0025 21.5 3.5 35 92-126 47-87 (153)
117 cd03455 SAV4209 SAV4209 is a S 24.3 2.1E+02 0.0047 18.7 5.2 15 116-130 100-114 (123)
118 PF10182 Flo11: Flo11 domain; 23.9 2.7E+02 0.0058 19.7 5.5 30 31-65 19-48 (152)
119 PRK13031 preprotein translocas 23.8 1.4E+02 0.003 21.3 3.6 45 50-94 53-102 (149)
120 PRK10626 hypothetical protein; 23.8 64 0.0014 24.8 2.1 34 1-36 1-34 (239)
121 PF06051 DUF928: Domain of Unk 23.7 2E+02 0.0043 21.1 4.7 30 94-123 86-116 (189)
122 COG5137 Histone chaperone invo 23.0 3.5E+02 0.0076 20.7 6.4 44 33-77 3-46 (279)
123 TIGR02738 TrbB type-F conjugat 23.0 42 0.00091 23.7 0.9 23 1-23 1-23 (153)
124 PRK11627 hypothetical protein; 22.7 1.6E+02 0.0035 21.8 4.0 9 1-9 1-9 (192)
125 TIGR03000 plancto_dom_1 Planct 22.4 2.1E+02 0.0046 17.9 4.9 35 91-125 32-67 (75)
126 PRK09934 fimbrial-like adhesin 22.0 1.5E+02 0.0033 21.1 3.7 14 1-14 1-14 (171)
127 TIGR03786 strep_pil_rpt strept 22.0 1.9E+02 0.0041 17.3 5.6 34 96-130 8-47 (64)
128 PF06280 DUF1034: Fn3-like dom 21.8 1.7E+02 0.0036 19.1 3.7 35 95-129 66-104 (112)
129 PF07213 DAP10: DAP10 membrane 21.7 75 0.0016 20.1 1.7 19 1-19 1-19 (79)
130 PF07411 DUF1508: Domain of un 21.4 1.4E+02 0.003 16.7 2.7 15 118-132 5-19 (49)
131 COG5294 Uncharacterized protei 21.1 1.4E+02 0.0031 20.1 3.1 37 1-38 1-38 (113)
132 PRK15209 long polar fimbrial p 20.9 2.1E+02 0.0047 20.2 4.3 24 33-56 27-52 (174)
133 PRK12618 flgA flagellar basal 20.6 36 0.00079 23.8 0.2 14 1-14 1-14 (141)
134 TIGR02588 conserved hypothetic 20.3 3E+02 0.0065 18.9 5.2 28 115-142 49-76 (122)
135 PF14054 DUF4249: Domain of un 20.3 4E+02 0.0086 20.3 12.0 15 48-62 37-51 (298)
No 1
>cd00917 PG-PI_TP The phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP) has been shown to bind phosphatidylglycerol and phosphatidylinositol, but the biological significance of this is still obscure. These proteins belong to the ML domain family.
Probab=100.00 E-value=1.9e-31 Score=184.11 Aligned_cols=116 Identities=38% Similarity=0.690 Sum_probs=108.9
Q ss_pred eeeCCCCCCccEEEeEEEEeCCCCCCCCcEEEEEEEEeCeEeccc-EEEEEEEECCEEeccCCcCCCCC-----CCCCCC
Q 032005 23 VKYCDKKKNYAVTIQQVKIIPDPVVTGKPATFNISAVTGQAVYGG-KVVINVAYFGVPVHQETRDVCEE-----VSCPIA 96 (149)
Q Consensus 23 ~~~C~~~~~~~~~i~~~~i~Pc~~~~G~~~~i~~~~~~~~~i~~~-~~~v~~~~~gi~v~~~~~d~C~~-----~~CPl~ 96 (149)
|++|+....+.++|++++++|||++||++++|++.|+++++++++ ++.+.+++++++++..+.|+|+. ..||++
T Consensus 1 ~~~C~~~~~~~~~i~~V~isP~p~~~G~~~ti~~~~~~~~~v~~g~~~~v~~~~~~i~~~~~~~DlC~~~~~~g~~CPi~ 80 (122)
T cd00917 1 FEYCDKGGEDIVKVTSVEISPNPPAAGQNLTIEASGSVGKEIEDGAYVVVEVKYGFIRLLSETYDLCDETKNVDLSCPIE 80 (122)
T ss_pred CccCCCCCCCeEEEEEEEEECCCcCCCCcEEEEEEEEECcCcCCCCEEEEEEEECCEEeecccCCcccccccCCCcCCcC
Confidence 789988765789999999999999999999999999999999997 88999999999999989999985 489999
Q ss_pred CCeEEEEEEEEcCCCCCCeeEEEEEEEEcCCCCEEEEEEEEE
Q 032005 97 AGDFVLSHTQTLPSFTPPGSYTLKMTMEDKNNEELTCFSFNF 138 (149)
Q Consensus 97 ~G~~~~~~~~~ip~~~P~g~~~v~~~l~d~~~~~~~C~~~~v 138 (149)
+|++.|..++.||+++|+|+|+++|+++|+++++++|++|++
T Consensus 81 ~G~~~~~~~~~ip~~~P~g~y~v~~~l~d~~~~~i~Ci~~~~ 122 (122)
T cd00917 81 PGDKFLTKLVDLPGEIPPGKYTVSARAYTKDDEEITCLSFSV 122 (122)
T ss_pred CCcEEEEEEeeCCCCCCCceEEEEEEEECCCCCEEEEEEeeC
Confidence 999779999999999999999999999999999999999975
No 2
>KOG4680 consensus Uncharacterized conserved protein, contains ML domain [General function prediction only]
Probab=99.97 E-value=6.4e-30 Score=174.91 Aligned_cols=132 Identities=50% Similarity=0.931 Sum_probs=126.1
Q ss_pred cCccceeeCCCCCCccEEEeEEEEeCCCCCCCCcEEEEEEEEeCeEecccEEEEEEEECCEEeccCCcCCCCCCCCCCCC
Q 032005 18 TQAIGVKYCDKKKNYAVTIQQVKIIPDPVVTGKPATFNISAVTGQAVYGGKVVINVAYFGVPVHQETRDVCEEVSCPIAA 97 (149)
Q Consensus 18 ~~~~~~~~C~~~~~~~~~i~~~~i~Pc~~~~G~~~~i~~~~~~~~~i~~~~~~v~~~~~gi~v~~~~~d~C~~~~CPl~~ 97 (149)
-.+.++.+|+....+.++|+.++++|.|+.||+++++++.++..+++..|+..+++.|+|+++..++.|+|+.+.||+++
T Consensus 22 ~~a~~~~yCd~~d~~~VkV~~Vni~PnP~a~Ge~aTf~i~~ntg~tIs~Gk~VIeV~y~gi~ihsethDLCdetsCPVep 101 (153)
T KOG4680|consen 22 NGATPVHYCDINDEYEVKVKEVNISPNPPARGENATFSISGNTGETISEGKYVIEVSYGGIRIHSETHDLCDETSCPVEP 101 (153)
T ss_pred cCCCcchhhhhcccceEEEEEEecCCCCCCCCCccEEEEecccccEeeCCeEEEEEEEeeEEEeeccccccccccCCcCc
Confidence 45789999998877799999999999999999999999999999999999988999999999999999999999999999
Q ss_pred CeEEEEEEEEcCCCCCCeeEEEEEEEEcCCCCEEEEEEEEEEEcccccccCC
Q 032005 98 GDFVLSHTQTLPSFTPPGSYTLKMTMEDKNNEELTCFSFNFKIGFHSLVSDS 149 (149)
Q Consensus 98 G~~~~~~~~~ip~~~P~g~~~v~~~l~d~~~~~~~C~~~~v~i~~~~~~~~~ 149 (149)
|+|....++.+|...|+|+|.++++++|++|+++.|+.|.+.|..+++|-|+
T Consensus 102 G~f~~~hsq~LPg~tPPG~Y~lkm~~~d~~~~~LTCisfsf~i~~g~~v~~~ 153 (153)
T KOG4680|consen 102 GDFLVAHSQVLPGYTPPGSYVLKMTAYDAKGKELTCISFSFDIGFGSSVADQ 153 (153)
T ss_pred CceeeeeeEeccCcCCCceEEEEEEeecCCCCEEEEEEEEEEeeccceeccC
Confidence 9999999999999999999999999999999999999999999999988764
No 3
>cd00918 Der-p2_like Several group 2 allergen proteins belong to the ML domain family. They include Dermatophagoides pteronyssinus, group 2 (Der p 2) and D. farinae, group 2 (Der f 2) allergens. These house dust mites cause heavy atopic diseases such as asthma and dermatitis. Although the allergenic properties of these proteins have been well characterized, their biological function in mites is unknown.
Probab=99.97 E-value=4.1e-30 Score=176.55 Aligned_cols=117 Identities=21% Similarity=0.314 Sum_probs=108.7
Q ss_pred eeeCCCCCCccEEEeEEEEeCCCCCCCCcEEEEEEEEeCeEecccEEEEEEEECCEEeccC--CcCCCCCCCCCCCCCe-
Q 032005 23 VKYCDKKKNYAVTIQQVKIIPDPVVTGKPATFNISAVTGQAVYGGKVVINVAYFGVPVHQE--TRDVCEEVSCPIAAGD- 99 (149)
Q Consensus 23 ~~~C~~~~~~~~~i~~~~i~Pc~~~~G~~~~i~~~~~~~~~i~~~~~~v~~~~~gi~v~~~--~~d~C~~~~CPl~~G~- 99 (149)
|++|+++....++|++|+-.||.++||++++++++|+++++.+++++.+.+.++|+++|++ +.|+|+.+.||+++|+
T Consensus 1 f~~Cg~~~~~~V~V~~C~~~pC~l~rG~~~~~~~~F~~~~~s~~l~~~v~a~~~gv~iP~p~~~~daC~~l~CPl~~G~~ 80 (120)
T cd00918 1 FKDCGKGEIKSLEVDGCSGDYCVIHRGKPLTLEAKFTANQDTAKAKIKITASIDGLEIDVPGIETDGCKYVKCPIKKGQH 80 (120)
T ss_pred CeeCCCCCcCEEEeCCCCCCCCEEECCCeEEEEEEEECCCccceEEEEEEEEECCEEcCCCCCCCCCcccEeCCCcCCcE
Confidence 6899987666889999999999999999999999999999999999999999999998877 7899988999999999
Q ss_pred EEEEEEEEcCCCCCCeeEEEEEEEEcCCCCEEEEEEEEEEE
Q 032005 100 FVLSHTQTLPSFTPPGSYTLKMTMEDKNNEELTCFSFNFKI 140 (149)
Q Consensus 100 ~~~~~~~~ip~~~P~g~~~v~~~l~d~~~~~~~C~~~~v~i 140 (149)
|+|+++++|++.||..+++++|+|+|++| .++||+++.+|
T Consensus 81 ~~y~~~~~V~~~~P~v~~~V~~~L~d~~g-~~~Cf~~~~~~ 120 (120)
T cd00918 81 YDIKYTWNVPAILPKIKAVVKAVLIGDHG-VLACGIVNGEV 120 (120)
T ss_pred EEEEEeeeccccCCCeEEEEEEEEEcCCC-cEEEEEEcCcC
Confidence 99999999999999999999999999888 59999998654
No 4
>cd00916 Npc2_like Niemann-Pick type C2 (Npc2) is a lysosomal protein in which a mutation in the gene causes a rare form of Niemann-Pick type C disease, an autosomal recessive lipid storage disorder characterized by accumulation of low-density lipoprotein-derived cholesterol in lysosomes. Although Npc2 is known to bind cholesterol, the function of this protein is unknown. These proteins belong to the ML domain family.
Probab=99.97 E-value=6e-30 Score=176.84 Aligned_cols=116 Identities=23% Similarity=0.397 Sum_probs=107.9
Q ss_pred eeeCCCC--CCccEEEeEEEEeCCCCCCCCcEEEEEEEEeCeEecccEEEEEEEECCEEeccC--CcCCCCC--CCCCCC
Q 032005 23 VKYCDKK--KNYAVTIQQVKIIPDPVVTGKPATFNISAVTGQAVYGGKVVINVAYFGVPVHQE--TRDVCEE--VSCPIA 96 (149)
Q Consensus 23 ~~~C~~~--~~~~~~i~~~~i~Pc~~~~G~~~~i~~~~~~~~~i~~~~~~v~~~~~gi~v~~~--~~d~C~~--~~CPl~ 96 (149)
|++|+++ ....++|++|+..||+++||+++++++.|+++++++++++.+.+.++|+++|++ +.|+|+. ..||++
T Consensus 1 ~~~Cg~~~~~~~~V~i~~C~~~PC~l~rG~~~~~~i~F~~~~~~~~~~~~v~~~~~gv~ip~~~~~~daC~~~~~~CPl~ 80 (123)
T cd00916 1 FRDCGSSRPTPSEVRISGCATLPCKLKRGSTAKVSIDFTPNFDSTSLKTEVHAILLGVPVPFPLPNPDACKNLGTSCPLS 80 (123)
T ss_pred CccCCCCCCceeEEEECCCCCCCCEEECCCEEEEEEEEEcCcccceeEEEEEEEECCEEecCCCCCCccccCCCCCCCCc
Confidence 6899876 346889999999999999999999999999999999999999999999999988 7899986 899999
Q ss_pred CCe-EEEEEEEEcCCCCCCeeEEEEEEEEcCCCCEEEEEEEEE
Q 032005 97 AGD-FVLSHTQTLPSFTPPGSYTLKMTMEDKNNEELTCFSFNF 138 (149)
Q Consensus 97 ~G~-~~~~~~~~ip~~~P~g~~~v~~~l~d~~~~~~~C~~~~v 138 (149)
+|+ |+|+++++|++.||.++++++|+|+|++++.++||++++
T Consensus 81 ~G~~~~y~~~~~v~~~~P~i~~~v~~~L~d~~~~~~~Cf~~~~ 123 (123)
T cd00916 81 AGEDVTYTLSLPVLAPYPGISVTVEWELTDDDGQVLTCFQIPA 123 (123)
T ss_pred CCcEEEEEEeeeccccCCCeEEEEEEEEEcCCCCEEEEEEeeC
Confidence 999 999999999999999999999999999888999999984
No 5
>smart00737 ML Domain involved in innate immunity and lipid metabolism. ML (MD-2-related lipid-recognition) is a novel domain identified in MD-1, MD-2, GM2A, Npc2 and multiple proteins of unknown function in plants, animals and fungi. These single-domain proteins were predicted to form a beta-rich fold containing multiple strands, and to mediate diverse biological functions through interacting with specific lipids.
Probab=99.97 E-value=3.9e-29 Score=171.45 Aligned_cols=113 Identities=35% Similarity=0.620 Sum_probs=103.6
Q ss_pred eeeCCCCCCccEEEeEEEEeCCCCCCCCcEEEEEEEEeCeEecccEEEEEEEECCEEeccC--CcCCCCCC--CCCCCCC
Q 032005 23 VKYCDKKKNYAVTIQQVKIIPDPVVTGKPATFNISAVTGQAVYGGKVVINVAYFGVPVHQE--TRDVCEEV--SCPIAAG 98 (149)
Q Consensus 23 ~~~C~~~~~~~~~i~~~~i~Pc~~~~G~~~~i~~~~~~~~~i~~~~~~v~~~~~gi~v~~~--~~d~C~~~--~CPl~~G 98 (149)
|++|+++ ..+|.+++++||+++||++++|++.|+++++++++++++.++++|+++|++ +.|+|+.. .||+++|
T Consensus 1 ~~~C~~~---~~~i~~v~v~Pc~~~~g~~~~i~i~f~~~~~~~~~~~~v~~~~~g~~ip~~~~~~d~C~~~~~~CPl~~G 77 (118)
T smart00737 1 FKDCGSN---PGQISSVSISPCPPVRGKTLTISISFTLNEDISKLKVVVHVKIGGIEVPIPGETYDLCKLLGSKCPIEKG 77 (118)
T ss_pred CccCCCC---CceEEEEEecCCCCCCCCEEEEEEEEEEcccceEEEEEEEEEECCEEEeccCCCCCccccCCCCCCCCCC
Confidence 7899874 458999999999999999999999999999999999999999999776655 78999864 8999999
Q ss_pred e-EEEEEEEEcCCCCCCeeEEEEEEEEcCCCCEEEEEEEEE
Q 032005 99 D-FVLSHTQTLPSFTPPGSYTLKMTMEDKNNEELTCFSFNF 138 (149)
Q Consensus 99 ~-~~~~~~~~ip~~~P~g~~~v~~~l~d~~~~~~~C~~~~v 138 (149)
+ +.|+.++.||+.+|+|+|+++|+++|++++.++|+++++
T Consensus 78 ~~~~~~~~~~v~~~~P~~~~~v~~~l~d~~~~~i~C~~~~~ 118 (118)
T smart00737 78 ETVNYTNSLTVPGIFPPGKYTVKWELTDEDGEELACINFTV 118 (118)
T ss_pred eeEEEEEeeEccccCCCeEEEEEEEEEcCCCCEEEEEEccC
Confidence 9 789999999999999999999999999999999999874
No 6
>PF02221 E1_DerP2_DerF2: ML domain; InterPro: IPR003172 The MD-2-related lipid-recognition (ML) domain is implicated in lipid recognition, particularly in the recognition of pathogen related products. It has an immunoglobulin-like beta-sandwich fold similar to that of E-set Ig domains. This domain is present in the following proteins: Epididymal secretory protein E1 (also known as Niemann-Pick C2 protein), which is known to bind cholesterol. Niemann-Pick disease type C2 is a fatal hereditary disease characterised by accumulation of low-density lipoprotein-derived cholesterol in lysosomes []. House-dust mite allergen proteins such as Der f 2 from Dermatophagoides farinae and Der p 2 from Dermatophagoides pteronyssinus []. ; PDB: 2AG9_B 1G13_B 2AG2_B 2AG4_A 1TJJ_C 1PU5_C 1PUB_A 2AF9_A 3T6Q_D 3M7O_B ....
Probab=99.96 E-value=6.5e-29 Score=173.31 Aligned_cols=121 Identities=34% Similarity=0.670 Sum_probs=109.3
Q ss_pred ccceeeCCCCCCccEEEeEEEEe-CCCCCCCCcEEEEEEE-EeCeEecccEEEEEEEECC-EEeccC----CcCCCCC--
Q 032005 20 AIGVKYCDKKKNYAVTIQQVKII-PDPVVTGKPATFNISA-VTGQAVYGGKVVINVAYFG-VPVHQE----TRDVCEE-- 90 (149)
Q Consensus 20 ~~~~~~C~~~~~~~~~i~~~~i~-Pc~~~~G~~~~i~~~~-~~~~~i~~~~~~v~~~~~g-i~v~~~----~~d~C~~-- 90 (149)
+++|++|+++....++|++++++ ||+++||++++|++.| +++++.+.+.+.+.+.++| +++|++ ..|+|+.
T Consensus 1 ~v~~~~C~~~~~~~~~v~~v~i~~pC~~~~g~~~~i~~~f~~~~~~~~~~~~~v~~~~~g~~~ip~~g~~~~~d~C~~~~ 80 (134)
T PF02221_consen 1 AVNFKDCGDGKDSPGTVTSVDISPPCPLKRGQPVTITIDFNTSKKDSDGLKVKVEAKVGGWIPIPFPGLCEYYDLCDNLF 80 (134)
T ss_dssp EEEEEESSSCTSSCECEEEEEEESSEEEETTSEEEEEEEEEECSSBBSSEEEEEEEEETTEEEEEEESSSCEEEEEGTSC
T ss_pred CcEEEECCCcccCCceeEEEEECCCCcccCCCEEEEEEEEEEccccccCCEEEEEEEECCcEEEccccccCccchhhhcc
Confidence 37899998754457889999998 9999999999999999 7877888888999999998 898886 3499993
Q ss_pred ---CCCCCCCCe-EEEEEEEEcCCCCCCeeEEEEEEEEcCCCCEEEEEEEEEEE
Q 032005 91 ---VSCPIAAGD-FVLSHTQTLPSFTPPGSYTLKMTMEDKNNEELTCFSFNFKI 140 (149)
Q Consensus 91 ---~~CPl~~G~-~~~~~~~~ip~~~P~g~~~v~~~l~d~~~~~~~C~~~~v~i 140 (149)
.+||+++|+ |+|++++.+|+.+|.|+|+++|+++|++|++++|++|+++|
T Consensus 81 ~~~~~CPi~~G~~~~~~~~~~i~~~~p~~~~~i~~~l~d~~~~~i~C~~~~v~I 134 (134)
T PF02221_consen 81 GNGLSCPIKAGEYYTYTYTIPIPKIYPPGKYTIQWKLTDQDGEEIACFEFPVKI 134 (134)
T ss_dssp CSSTTSTBTTTEEEEEEEEEEESTTSSSEEEEEEEEEEETTTEEEEEEEEEEEE
T ss_pred cccccCccCCCcEEEEEEEEEcccceeeEEEEEEEEEEeCCCCEEEEEEEEeEC
Confidence 599999999 69999999999999999999999999998999999999987
No 7
>KOG4063 consensus Major epididymal secretory protein HE1 [Function unknown]
Probab=99.96 E-value=1.8e-28 Score=170.40 Aligned_cols=128 Identities=25% Similarity=0.430 Sum_probs=113.6
Q ss_pred hhccCccceeeCCCC--CCccEEEeEEEEeCCCCCCCCcEEEEEEEEeCeEecccEEEEEEEECC-EEeccC--CcCCCC
Q 032005 15 VSSTQAIGVKYCDKK--KNYAVTIQQVKIIPDPVVTGKPATFNISAVTGQAVYGGKVVINVAYFG-VPVHQE--TRDVCE 89 (149)
Q Consensus 15 ~~~~~~~~~~~C~~~--~~~~~~i~~~~i~Pc~~~~G~~~~i~~~~~~~~~i~~~~~~v~~~~~g-i~v~~~--~~d~C~ 89 (149)
.+.+..+.+++|++. ....++|++|..+||.++||+..+|+++|.++++.+..+..+.....| +++|++ ..|+|.
T Consensus 19 ~aq~~~t~~k~C~ss~g~~~~V~i~~C~t~pC~lkKgt~~si~I~F~~~~~~~~lkt~v~g~~lg~v~vPfpl~~~dacv 98 (158)
T KOG4063|consen 19 AAQAISTGVKQCGSSDGTPLEVKIDGCPTTPCQLKKGTEASIQIDFAPSRDTTKLKTVVHGITLGSVPVPFPLPASDACV 98 (158)
T ss_pred hhcccCcccccccCCCCcceEEEecCCCCCceEEecCCeEEEEEEEeeccchhhhhheeeeeecccEeecCCCCCCcccc
Confidence 344668999999984 335889999999999999999999999999999999998888777666 888887 678885
Q ss_pred ------CCCCCCCCCe-EEEEEEEEcCCCCCCeeEEEEEEEEcCCCCEEEEEEEEEEEcc
Q 032005 90 ------EVSCPIAAGD-FVLSHTQTLPSFTPPGSYTLKMTMEDKNNEELTCFSFNFKIGF 142 (149)
Q Consensus 90 ------~~~CPl~~G~-~~~~~~~~ip~~~P~g~~~v~~~l~d~~~~~~~C~~~~v~i~~ 142 (149)
+..||+.+|+ |+|..+++|-..+|.+...++|+|.|+||+...||+++++|..
T Consensus 99 ~~~l~~gv~CPl~age~ytY~~slpI~~~yP~v~v~iew~L~D~d~~~~~Cf~ipakIk~ 158 (158)
T KOG4063|consen 99 CGNLLHGVYCPLSAGEDYTYLNSLPITENYPEVSVIIEWQLQDQDNEKAVCFEIPAKIKK 158 (158)
T ss_pred cccccccccCcccCCCceEEEEEeeccccCCceeEEEEEEEecCCCCeEEEEEEEeeecC
Confidence 2789999999 9999999999999999999999999999999999999999863
No 8
>cd00912 ML The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2 and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids.
Probab=99.95 E-value=1.2e-26 Score=161.08 Aligned_cols=115 Identities=18% Similarity=0.347 Sum_probs=100.7
Q ss_pred eeeCCCCCC--ccEEEeEEEEeCCCCCCCCcEEEEEEEEeCeEecccEEEEEEEECCEEeccC--CcCCCCC-----CCC
Q 032005 23 VKYCDKKKN--YAVTIQQVKIIPDPVVTGKPATFNISAVTGQAVYGGKVVINVAYFGVPVHQE--TRDVCEE-----VSC 93 (149)
Q Consensus 23 ~~~C~~~~~--~~~~i~~~~i~Pc~~~~G~~~~i~~~~~~~~~i~~~~~~v~~~~~gi~v~~~--~~d~C~~-----~~C 93 (149)
|++|+++.. ..++|+.|+-.||+++||++++++++|+++++++++++.+.++++|+++|++ ..|+|+. ..|
T Consensus 1 ~~~C~~~~~~i~~V~v~pc~~~pC~~~~g~~~~i~~~f~~~~~~~~~~~~v~~~~~gi~~p~~~~~~d~C~~~~~~~~~C 80 (127)
T cd00912 1 LVDCSDNSANIKEVLLSPCDPLPCPDHRGGNYNLSVTGTLREDIKSLYVDLALMSQGIKVLNPDNSYDFCEAGLPKPSFC 80 (127)
T ss_pred CcccCCCCCceeEEEeCCCCCCCCcccCCCeEEEEEEEEECccccEEEEEEEEEECCEEeccCCCCCCcccccCcccccC
Confidence 789987521 2455555555566999999999999999999999999999999999999987 7899975 489
Q ss_pred CCCCCe-EEEEEEEEcCC-CCCCeeEEEEEEEEcCCCCEEEEEEEE
Q 032005 94 PIAAGD-FVLSHTQTLPS-FTPPGSYTLKMTMEDKNNEELTCFSFN 137 (149)
Q Consensus 94 Pl~~G~-~~~~~~~~ip~-~~P~g~~~v~~~l~d~~~~~~~C~~~~ 137 (149)
|+++|+ |+|+.+++||+ .+|++.|+++|++.|++|++++|++++
T Consensus 81 Pl~~G~~~~~~~~~~v~~~~~P~~~~~v~~~l~~~~~~~v~C~~~~ 126 (127)
T cd00912 81 PLRKGQQYSYAKTVNVPEFTIPTIEYQVVLEDVTDKGEVLACAQAT 126 (127)
T ss_pred CcCCCCEEEEEEEEecCcccCCCeeEEEEEEEEcCCCCEEEEEecc
Confidence 999995 99999999997 899999999999999989999999986
No 9
>cd00915 MD-1_MD-2 MD-1 and MD-2 are cofactors required for LPS signaling through cell surface receptors. MD-2 and its binding partner, Toll-like receptor 4 (TLR4), are essential for the innate immune responses of mammalian cells to bacterial lipopolysaccharide (LPS); MD-2 directly binds the lipid A moiety of LPS. The TLR4-like receptor, RP105, which mediates LPS-induced lymphocyte proliferation, interacts with MD-1; MD-1 enhances RP105-mediated LPS-induced growth of B cells. These proteins belong to the ML domain family.
Probab=99.91 E-value=1.2e-23 Score=145.28 Aligned_cols=112 Identities=15% Similarity=0.243 Sum_probs=99.5
Q ss_pred ccceeeCCCCCCccEEEeEEEEeCCCCCCCCcEEEEEEEEeCeEecccEEEEEEEECCEEeccC-CcCCCCC-----CCC
Q 032005 20 AIGVKYCDKKKNYAVTIQQVKIIPDPVVTGKPATFNISAVTGQAVYGGKVVINVAYFGVPVHQE-TRDVCEE-----VSC 93 (149)
Q Consensus 20 ~~~~~~C~~~~~~~~~i~~~~i~Pc~~~~G~~~~i~~~~~~~~~i~~~~~~v~~~~~gi~v~~~-~~d~C~~-----~~C 93 (149)
.+.|+.|+.-. .=+++++||.++||++++|+++|+++++++++.+.|.+..+|+++| + ...+|++ ..|
T Consensus 10 ~~~y~~cd~~~-----~~~~~~~pC~l~rg~n~~I~~~f~~~~d~~~L~~~v~~~~~g~~lP-~~~e~~C~~g~~~~s~C 83 (130)
T cd00915 10 EFSYSSCDPMQ-----DFSFSAEPCSTLKGTNGFIRIKFILRRDIKELYFNLSLNVNGIEVL-TRSEIICHGYLDKYSFC 83 (130)
T ss_pred EEEeeeCCchh-----eeEeecccccceeCCcEEEEEEEEECcccceeEEEEEEEECCccCC-CCCcccccCCCcccccC
Confidence 47899998753 2488999999999999999999999999999999999999999888 5 2339984 699
Q ss_pred CCCCCe-EEEE--EEEEcCCCCCCeeEEEEEEEEcCCCCEEEEEEEEE
Q 032005 94 PIAAGD-FVLS--HTQTLPSFTPPGSYTLKMTMEDKNNEELTCFSFNF 138 (149)
Q Consensus 94 Pl~~G~-~~~~--~~~~ip~~~P~g~~~v~~~l~d~~~~~~~C~~~~v 138 (149)
|+++|+ |+|. .++++.+ ||.++|+++|+|+|++++.++|++|.+
T Consensus 84 P~~kGet~~Y~~p~slpi~~-yP~~~y~V~weL~d~~~~~l~Cf~~ti 130 (130)
T cd00915 84 GALKGETVYYVGPFSFKGIL-IPQGQYRCVAELIVENRETVACANFTI 130 (130)
T ss_pred CccCCceEEEeeeecccccc-cCCccEEEEEEEECCCCCEEEEEEEEC
Confidence 999999 8999 8888888 999999999999999999999999864
No 10
>cd00258 GM2-AP GM2 activator protein (GM2-AP) is a non-enzymatic lysosomal protein that acts as cofactor in the sequential degradation of gangliosides. GM2A is an essential cofactor for beta-hexosaminidase A (Hex A) in the enzymatic hydrolysis of GM2 ganglioside to GM3. Mutation of the gene results in the AB variant of Tay-Sachs disease. GM2-AP and similar proteins belong to the ML domain family.
Probab=99.83 E-value=3.3e-19 Score=126.49 Aligned_cols=121 Identities=22% Similarity=0.446 Sum_probs=98.8
Q ss_pred ccceeeCCCCCCccEEEeEEEEeCCCCCCCCcEEEEEEEEeCeEeccc-EEEEEE--EECCE--EeccC-------CcCC
Q 032005 20 AIGVKYCDKKKNYAVTIQQVKIIPDPVVTGKPATFNISAVTGQAVYGG-KVVINV--AYFGV--PVHQE-------TRDV 87 (149)
Q Consensus 20 ~~~~~~C~~~~~~~~~i~~~~i~Pc~~~~G~~~~i~~~~~~~~~i~~~-~~~v~~--~~~gi--~v~~~-------~~d~ 87 (149)
...|++|+.+.+ .+.|++++++|.|+.+++++++++.++..+++.++ ++.+.+ .+.|+ ++|-. ..|+
T Consensus 2 ~fsW~nCg~~~d-p~~i~sl~l~PdPi~ipg~~tvs~~~~~~~~lsSp~~~~l~v~k~v~g~Wi~iPC~~~~GSCty~d~ 80 (162)
T cd00258 2 GFSWSNCDGESL-PAVIKSLTVNPDPINIPGDLTVSTVGSTSVPLSSPLKVILTLEKEVAGLWMKIPCLDNIGSCTYDNA 80 (162)
T ss_pred CcccccCCCCCC-ceEEeeeEEcCCCcccCCcEEEEEEEEEeeEcCCCcEEEEEEEeecccEEEEcccccccCcccccch
Confidence 368999998754 88999999999999999999999999999999987 665544 44554 44421 4578
Q ss_pred CCCC---------------------CCCCCCCeEEEEEEE-Ec-----CCCCCCeeEEEEEEEEcCCCCEEEEEEEEEEE
Q 032005 88 CEEV---------------------SCPIAAGDFVLSHTQ-TL-----PSFTPPGSYTLKMTMEDKNNEELTCFSFNFKI 140 (149)
Q Consensus 88 C~~~---------------------~CPl~~G~~~~~~~~-~i-----p~~~P~g~~~v~~~l~d~~~~~~~C~~~~v~i 140 (149)
|+.. +||+++|+|++..+. .| |++++.|+|+++..+ +++|++++|+++.+.+
T Consensus 81 C~~l~~~~~~~~~Cp~~l~~~g~pC~CP~~~G~y~lp~s~f~lP~~~LPs~l~~G~Y~i~~~l-~~~g~~l~C~~~~~sL 159 (162)
T cd00258 81 CDLLDTLIPPGQQCPEPLRTYGLPCHCPFKEGVYSLPDSTFTLPNVDLPSWLTNGNYRITGIL-MADGKELGCGKFTFSL 159 (162)
T ss_pred hhchhcccCCCCCCCchhhccCCccCCCCCCcceEccceeeecccccCCCccCCCcEEEEEEE-CCCCCEEEEEEEEEEE
Confidence 8631 699999999874443 55 889999999999999 7889999999999998
Q ss_pred cc
Q 032005 141 GF 142 (149)
Q Consensus 141 ~~ 142 (149)
.+
T Consensus 160 ~~ 161 (162)
T cd00258 160 ES 161 (162)
T ss_pred ec
Confidence 75
No 11
>PF14558 TRP_N: ML-like domain
Probab=98.79 E-value=1.3e-07 Score=66.74 Aligned_cols=119 Identities=20% Similarity=0.380 Sum_probs=83.0
Q ss_pred ccceeeCCCCCCccEEEeEEEEeCCCCCCCCcEEEEEEEEeCeEecccEEEEEEEECCEEeccCCcCCCCC---CCCCCC
Q 032005 20 AIGVKYCDKKKNYAVTIQQVKIIPDPVVTGKPATFNISAVTGQAVYGGKVVINVAYFGVPVHQETRDVCEE---VSCPIA 96 (149)
Q Consensus 20 ~~~~~~C~~~~~~~~~i~~~~i~Pc~~~~G~~~~i~~~~~~~~~i~~~~~~v~~~~~gi~v~~~~~d~C~~---~~CPl~ 96 (149)
...|.+|.++. .+.++.+++.-.| ..+++.+++.++....-...++.+.+...|..+.....|.|+. ..||+.
T Consensus 4 t~~f~~Cl~~s--~~~~~~Fdv~~~~--~n~tl~~~v~G~s~~~~~~vtl~~~v~ayg~~~~~~~~d~C~~~~~~lCPl~ 79 (141)
T PF14558_consen 4 TSSFSNCLDNS--YFTASRFDVTYDP--DNRTLVFDVYGNSSISNKYVTLFISVNAYGYTPYNETFDPCDSNVPGLCPLP 79 (141)
T ss_pred eCChhHcCCcc--ccceEEEeEEEcC--CCCEEEEEEEEEeccCCcEEEEEEEEEeeccccccccCCcccCCCCcccccc
Confidence 46789998874 5566666654332 3468888888887664333455677776777776778999984 579999
Q ss_pred CCeEEEEEEEEc---------CCC---CCCeeEEEEEEEEcC-CCCEEEEEEEEEEEcc
Q 032005 97 AGDFVLSHTQTL---------PSF---TPPGSYTLKMTMEDK-NNEELTCFSFNFKIGF 142 (149)
Q Consensus 97 ~G~~~~~~~~~i---------p~~---~P~g~~~v~~~l~d~-~~~~~~C~~~~v~i~~ 142 (149)
||......+..+ |.+ +|.-..++++++.+. ++++++|++..++-..
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~ip~iay~~pdl~a~~~v~~~~~~~~~~iaCv~a~ltng~ 138 (141)
T PF14558_consen 80 PGFFAIASSQIIVPPSFTSQIPSIAYAFPDLDATVRVILGDTDTGTQIACVQATLTNGK 138 (141)
T ss_pred ccccccccccccCCHHHhhcCCceeEEcCCceEEEEEEEccCCCCCEEEEEEEEEECCC
Confidence 998544433333 221 466666778888887 6889999999887544
No 12
>PF15418 DUF4625: Domain of unknown function (DUF4625)
Probab=97.62 E-value=0.0019 Score=45.08 Aligned_cols=104 Identities=19% Similarity=0.256 Sum_probs=68.5
Q ss_pred EEeEEEEeC----C-CCCCCCcEEEEEEEEeCeEecccEEEEEEEECCEEeccCCcCCCCC-----CCCCCCCC--eEEE
Q 032005 35 TIQQVKIIP----D-PVVTGKPATFNISAVTGQAVYGGKVVINVAYFGVPVHQETRDVCEE-----VSCPIAAG--DFVL 102 (149)
Q Consensus 35 ~i~~~~i~P----c-~~~~G~~~~i~~~~~~~~~i~~~~~~v~~~~~gi~v~~~~~d~C~~-----~~CPl~~G--~~~~ 102 (149)
.|+..++.. | ..++|+++.+++.++.+..+.+-++++.-.+.+..=- .....|.. ..=.+..| .+.+
T Consensus 16 ~I~~~~~~~~p~~~~~~~~G~~ihfe~~i~d~~~i~si~VeIH~nfd~H~h~-~~~~~~~~~~~~~~~~~~~~g~~~~~~ 94 (132)
T PF15418_consen 16 VITLNEIGAFPENCKVATRGDDIHFEADISDNSAIKSIKVEIHNNFDHHTHS-TEAGECEKPWVFEQDYDIYGGKKNYDF 94 (132)
T ss_pred EEEeeecccCCCCCeEEecCCcEEEEEEEEcccceeEEEEEEecCcCccccc-ccccccccCcEEEEEEcccCCcccEeE
Confidence 455555433 3 3799999999999999999887777774433331000 01112221 00023334 4889
Q ss_pred EEEEEcCCCCCCeeEEEEEEEEcCCCCEEEEEEEEEEE
Q 032005 103 SHTQTLPSFTPPGSYTLKMTMEDKNNEELTCFSFNFKI 140 (149)
Q Consensus 103 ~~~~~ip~~~P~g~~~v~~~l~d~~~~~~~C~~~~v~i 140 (149)
+..+.||...++|.|++.++++|+.|.+.. ....++|
T Consensus 95 h~~i~IPa~a~~G~YH~~i~VtD~~Gn~~~-~~~~i~I 131 (132)
T PF15418_consen 95 HEHIDIPADAPAGDYHFMITVTDAAGNQTE-EERSIKI 131 (132)
T ss_pred EEeeeCCCCCCCcceEEEEEEEECCCCEEE-EEEEEEE
Confidence 999999999999999999999999986643 4444444
No 13
>smart00697 DM8 Repeats found in several Drosophila proteins.
Probab=96.72 E-value=0.012 Score=37.84 Aligned_cols=36 Identities=36% Similarity=0.707 Sum_probs=28.3
Q ss_pred CCCCCCCCeEEE-EEEE---EcCCCCCCeeEEEEEEEEcC
Q 032005 91 VSCPIAAGDFVL-SHTQ---TLPSFTPPGSYTLKMTMEDK 126 (149)
Q Consensus 91 ~~CPl~~G~~~~-~~~~---~ip~~~P~g~~~v~~~l~d~ 126 (149)
..||+++|.|.+ ...+ .+|..+|.|.|.+++++...
T Consensus 40 ~~CP~~~g~y~~~n~~l~~~~~p~~lP~G~y~~~~~~~~~ 79 (93)
T smart00697 40 DTCPLPKGHYYLRNFRLDENLLPSFLPDGDYRLNLTFFFG 79 (93)
T ss_pred CCCCCcCCeEEEEeeEeCcccCCccCCCeeEEEEEEEEcC
Confidence 479999999644 2232 47889999999999999865
No 14
>PF14524 Wzt_C: Wzt C-terminal domain; PDB: 2R5O_B.
Probab=96.12 E-value=0.094 Score=35.83 Aligned_cols=89 Identities=17% Similarity=0.310 Sum_probs=53.7
Q ss_pred cEEEeEEEEeC-----C-CCCCCCcEEEEEEEEeCeEecccEEEEEEEE-CCEEeccCCcCCCCCCCCCC-CCCeEEEEE
Q 032005 33 AVTIQQVKIIP-----D-PVVTGKPATFNISAVTGQAVYGGKVVINVAY-FGVPVHQETRDVCEEVSCPI-AAGDFVLSH 104 (149)
Q Consensus 33 ~~~i~~~~i~P-----c-~~~~G~~~~i~~~~~~~~~i~~~~~~v~~~~-~gi~v~~~~~d~C~~~~CPl-~~G~~~~~~ 104 (149)
.++|+++.+.. + .+..|+++.|++.+..++++....+.+.+.- .|..+...+. ......-+. ++|.+++..
T Consensus 12 ~~~I~~v~i~~~~g~~~~~~~~ge~~~i~i~~~~~~~i~~~~~~~~i~~~~g~~v~~~~t-~~~~~~~~~~~~g~~~~~~ 90 (142)
T PF14524_consen 12 EARITSVRILDSDGEPTSSFESGEPIRIRIDYEVNEDIDDPVFGFAIRDSDGQRVFGTNT-YDSGFPIPLSEGGTYEVTF 90 (142)
T ss_dssp SEEEEEEEEEETTEES-SSEETTSEEEEEEEEEESS-EEEEEEEEEEEETT--EEEEEEH-HHHT--EEE-TT-EEEEEE
T ss_pred CEEEEEEEEEeCCCCEeeEEeCCCEEEEEEEEEECCCCCccEEEEEEEcCCCCEEEEECc-cccCccccccCCCEEEEEE
Confidence 66788887654 2 4789999999999999999988766554433 3444432211 111111122 266677777
Q ss_pred EEEcCCCCCCeeEEEEEEEE
Q 032005 105 TQTLPSFTPPGSYTLKMTME 124 (149)
Q Consensus 105 ~~~ip~~~P~g~~~v~~~l~ 124 (149)
+++.+ +.+|+|.+.+.+.
T Consensus 91 ~i~~~--L~~G~Y~i~v~l~ 108 (142)
T PF14524_consen 91 TIPKP--LNPGEYSISVGLG 108 (142)
T ss_dssp EEE----B-SEEEEEEEEEE
T ss_pred EEcCc--cCCCeEEEEEEEE
Confidence 77766 7789999999993
No 15
>PF07705 CARDB: CARDB; InterPro: IPR011635 The APHP (acidic peptide-dependent hydrolases/peptidase) domain is found in a variety of different proteins.; PDB: 2KUT_A 2L0D_A 3IDU_A 2KL6_A.
Probab=95.39 E-value=0.31 Score=31.15 Aligned_cols=81 Identities=25% Similarity=0.479 Sum_probs=53.4
Q ss_pred cEEEeEEEEeCCCCCCCCcEEEEEEEEeCeEecccEEEEEEEECCEEeccCCcCCCCCCCCCCCCCe-EEEEEEEEcCCC
Q 032005 33 AVTIQQVKIIPDPVVTGKPATFNISAVTGQAVYGGKVVINVAYFGVPVHQETRDVCEEVSCPIAAGD-FVLSHTQTLPSF 111 (149)
Q Consensus 33 ~~~i~~~~i~Pc~~~~G~~~~i~~~~~~~~~i~~~~~~v~~~~~gi~v~~~~~d~C~~~~CPl~~G~-~~~~~~~~ip~~ 111 (149)
.+.| .....|..+..|+.+++++...-........+.+.+..+|..+-. ... =.|++|+ .++++++..+
T Consensus 3 DL~v-~~~~~~~~~~~g~~~~i~~~V~N~G~~~~~~~~v~~~~~~~~~~~--~~i-----~~L~~g~~~~v~~~~~~~-- 72 (101)
T PF07705_consen 3 DLTV-SITVSPSNVVPGEPVTITVTVKNNGTADAENVTVRLYLDGNSVST--VTI-----PSLAPGESETVTFTWTPP-- 72 (101)
T ss_dssp -EEE--EEEC-SEEETTSEEEEEEEEEE-SSS-BEEEEEEEEETTEEEEE--EEE-----SEB-TTEEEEEEEEEE-S--
T ss_pred CEEE-EEeeCCCcccCCCEEEEEEEEEECCCCCCCCEEEEEEECCceecc--EEE-----CCcCCCcEEEEEEEEEeC--
Confidence 3556 778888999999999999998877666566677888787765411 111 2378898 5677777766
Q ss_pred CCCeeEEEEEEEE
Q 032005 112 TPPGSYTLKMTME 124 (149)
Q Consensus 112 ~P~g~~~v~~~l~ 124 (149)
-+|.|++++.+-
T Consensus 73 -~~G~~~i~~~iD 84 (101)
T PF07705_consen 73 -SPGSYTIRVVID 84 (101)
T ss_dssp -S-CEEEEEEEES
T ss_pred -CCCeEEEEEEEe
Confidence 569999988883
No 16
>PF06477 DUF1091: Protein of unknown function (DUF1091); InterPro: IPR010512 This entry contains a number of proteins from Drosophila melanogaster and other insects. Their function is unknown.
Probab=95.27 E-value=0.028 Score=35.38 Aligned_cols=29 Identities=41% Similarity=0.894 Sum_probs=21.8
Q ss_pred CCCCCCCCeEEEE-EEE---EcCCCCCCeeEEE
Q 032005 91 VSCPIAAGDFVLS-HTQ---TLPSFTPPGSYTL 119 (149)
Q Consensus 91 ~~CPl~~G~~~~~-~~~---~ip~~~P~g~~~v 119 (149)
..||+++|.|.+. ..+ .+|+++|.|.|.+
T Consensus 49 ~~CP~~~g~Y~~~n~~~~~~~~P~~~p~G~y~i 81 (81)
T PF06477_consen 49 HTCPFKKGNYYLRNFTIDEKFLPSFLPEGDYRI 81 (81)
T ss_pred CCCCCCCCEEEEEEEEECcccCCCcCCCeEEEC
Confidence 4799999996543 333 4899999999864
No 17
>PF02115 Rho_GDI: RHO protein GDP dissociation inhibitor; InterPro: IPR000406 The GDP dissociation inhibitor for rho proteins, rho GDI, regulates GDP/GTP exchange by inhibiting the dissociation of GDP from them. The protein contains 204 amino acids, with a calculated Mr value of 23,421. Hydropathy analysis shows it to be largely hydrophilic, with a single hydrophobic region. Results of database searches suggest rho GDI is a novel protein, currently with no known homologue. The protein plays an important role in the activation of the superoxide (O2-)-generating NADPH oxidase of phagocytes. This process requires the interaction of membrane-associated cytochrome b559 with 3 cytosolic components: p47-phox, p67-phox and a heterodimer of the small G-protein p21rac1 and rho GDI []. The association of p21rac and GDI inhibits dissociation of GDP from p21rac, thereby maintaining it in an inactive form. The proteins are attached via a lipid tail on p21rac that binds to the hydrophobic region of GDI []. Dissociation of these proteins might be mediated by the release of lipids (e.g., arachidonate and phosphatidate) from membranes through the action of phospholipases []. The lipids may then compete with the lipid tail on p21rac for the hydrophobic pocket on GDI.; GO: 0005094 Rho GDP-dissociation inhibitor activity, 0005737 cytoplasm; PDB: 2JHV_A 2JHU_A 2JI0_A 2JHS_A 1RHO_A 2JHW_A 1FT3_A 2JHZ_B 1QVY_C 1FST_B ....
Probab=95.18 E-value=0.38 Score=35.89 Aligned_cols=94 Identities=19% Similarity=0.277 Sum_probs=58.2
Q ss_pred CCCCCcEEEEEEEEeCeEecc-cEEEEEEEECCEEeccCCcCCCCCCCCCCCCCeEEEEEEEE-cC-CCCCCeeEEEEEE
Q 032005 46 VVTGKPATFNISAVTGQAVYG-GKVVINVAYFGVPVHQETRDVCEEVSCPIAAGDFVLSHTQT-LP-SFTPPGSYTLKMT 122 (149)
Q Consensus 46 ~~~G~~~~i~~~~~~~~~i~~-~~~~v~~~~~gi~v~~~~~d~C~~~~CPl~~G~~~~~~~~~-ip-~~~P~g~~~v~~~ 122 (149)
++.|..+.+++.|..++++-+ +...-.++-.|+++-....- - |...|- ...|++.+.-. .| .++-.|+|+++-+
T Consensus 103 IKEGs~Y~l~i~F~V~~~ivsGL~Y~q~Vkr~Gi~Vdk~~~m-i-Gsy~P~-~e~y~~~~p~eeaPsG~laRG~Y~aks~ 179 (200)
T PF02115_consen 103 IKEGSKYRLKITFKVQHEIVSGLKYVQTVKRKGIPVDKREEM-I-GSYAPQ-TEPYEKTFPEEEAPSGMLARGSYTAKSK 179 (200)
T ss_dssp EETT-EEEEEEEEEE-SS-EEEEEEEEEEEETTEEEEEEEEE-E-EEE--E-SSEEEEEEEEEE--BSTTT-EEEEEEEE
T ss_pred ccCCCEEEEEEEEEECCccccCcEEEEEEEECCEeEccccee-e-eccCCC-CcceEEeCcCccCCCceeEeeeeeEEEE
Confidence 688999999999999997544 46555677788877432111 1 112222 12255544433 55 4567799999999
Q ss_pred EEcCCCCEEEEEEEEEEEcc
Q 032005 123 MEDKNNEELTCFSFNFKIGF 142 (149)
Q Consensus 123 l~d~~~~~~~C~~~~v~i~~ 142 (149)
++|++++...=++-.+.|.+
T Consensus 180 f~DdD~~~~l~~~w~feI~K 199 (200)
T PF02115_consen 180 FVDDDKNVHLEWEWSFEIKK 199 (200)
T ss_dssp EEETTSSECEEEEEEEEEES
T ss_pred EEeCCCcEEEEEEEEEEEec
Confidence 99998877667777777765
No 18
>PF10633 NPCBM_assoc: NPCBM-associated, NEW3 domain of alpha-galactosidase; InterPro: IPR018905 This domain has been named NEW3, but its function is not known. It is found on proteins which are bacterial galactosidases [].; PDB: 1EUT_A 2BZD_A 1WCQ_C 2BER_A 1W8O_A 1EUU_A 1W8N_A.
Probab=94.61 E-value=0.18 Score=31.49 Aligned_cols=72 Identities=19% Similarity=0.373 Sum_probs=40.8
Q ss_pred CCCCcEEEEEEEEeCeE--ecccEEEEEEEECCEEeccCCcCCCCCCCCCCCCCe-EEEEEEEEcCCCCCCeeEEEEEEE
Q 032005 47 VTGKPATFNISAVTGQA--VYGGKVVINVAYFGVPVHQETRDVCEEVSCPIAAGD-FVLSHTQTLPSFTPPGSYTLKMTM 123 (149)
Q Consensus 47 ~~G~~~~i~~~~~~~~~--i~~~~~~v~~~~~gi~v~~~~~d~C~~~~CPl~~G~-~~~~~~~~ip~~~P~g~~~v~~~l 123 (149)
..|+.+++++.++.+.. +....+.+.+ -.|+.+..... ... .|.+|+ .+.++.+.+|...++|+|.+.+++
T Consensus 2 ~~G~~~~~~~tv~N~g~~~~~~v~~~l~~-P~GW~~~~~~~----~~~-~l~pG~s~~~~~~V~vp~~a~~G~y~v~~~a 75 (78)
T PF10633_consen 2 TPGETVTVTLTVTNTGTAPLTNVSLSLSL-PEGWTVSASPA----SVP-SLPPGESVTVTFTVTVPADAAPGTYTVTVTA 75 (78)
T ss_dssp -TTEEEEEEEEEE--SSS-BSS-EEEEE---TTSE---EEE----EE---B-TTSEEEEEEEEEE-TT--SEEEEEEEEE
T ss_pred CCCCEEEEEEEEEECCCCceeeEEEEEeC-CCCccccCCcc----ccc-cCCCCCEEEEEEEEECCCCCCCceEEEEEEE
Confidence 47889999999887663 3344444444 24444211110 122 689998 689999999999999999998876
Q ss_pred E
Q 032005 124 E 124 (149)
Q Consensus 124 ~ 124 (149)
.
T Consensus 76 ~ 76 (78)
T PF10633_consen 76 R 76 (78)
T ss_dssp E
T ss_pred E
Confidence 4
No 19
>PLN00044 multi-copper oxidase-related protein; Provisional
Probab=94.45 E-value=0.26 Score=42.61 Aligned_cols=17 Identities=24% Similarity=0.436 Sum_probs=13.5
Q ss_pred CCCCCCCCCe-EEEEEEE
Q 032005 90 EVSCPIAAGD-FVLSHTQ 106 (149)
Q Consensus 90 ~~~CPl~~G~-~~~~~~~ 106 (149)
++.||++||+ |+|++..
T Consensus 102 ~TQcPI~PG~sftY~F~~ 119 (596)
T PLN00044 102 GTNCAIPAGWNWTYQFQV 119 (596)
T ss_pred CCcCCcCCCCcEEEEEEe
Confidence 4789999998 7776665
No 20
>PF04234 CopC: CopC domain; InterPro: IPR007348 CopC is a bacterial blue copper protein that binds 1 atom of copper per protein molecule. Along with CopA, CopC mediates copper resistance by sequestration of copper in the periplasm [].; GO: 0005507 copper ion binding, 0046688 response to copper ion, 0042597 periplasmic space; PDB: 1IX2_B 1LYQ_A 2C9P_C 2C9R_A 2C9Q_A 1M42_A 1OT4_A 1NM4_A.
Probab=94.14 E-value=0.28 Score=32.10 Aligned_cols=35 Identities=31% Similarity=0.588 Sum_probs=24.7
Q ss_pred EEEEEcCCCCCCeeEEEEEEEEcCCCCEE-EEEEEE
Q 032005 103 SHTQTLPSFTPPGSYTLKMTMEDKNNEEL-TCFSFN 137 (149)
Q Consensus 103 ~~~~~ip~~~P~g~~~v~~~l~d~~~~~~-~C~~~~ 137 (149)
.+.+.+|..+++|.|+|+|+....||..+ .=+.|.
T Consensus 60 ~~~~~l~~~l~~G~YtV~wrvvs~DGH~~~G~~~F~ 95 (97)
T PF04234_consen 60 TLTVPLPPPLPPGTYTVSWRVVSADGHPVSGSFSFT 95 (97)
T ss_dssp EEEEEESS---SEEEEEEEEEEETTSCEEEEEEEEE
T ss_pred EEEEECCCCCCCceEEEEEEEEecCCCCcCCEEEEE
Confidence 56667888899999999999999999764 334443
No 21
>PRK10301 hypothetical protein; Provisional
Probab=93.20 E-value=0.26 Score=33.93 Aligned_cols=29 Identities=17% Similarity=0.287 Sum_probs=24.2
Q ss_pred EEEEEcCCCCCCeeEEEEEEEEcCCCCEE
Q 032005 103 SHTQTLPSFTPPGSYTLKMTMEDKNNEEL 131 (149)
Q Consensus 103 ~~~~~ip~~~P~g~~~v~~~l~d~~~~~~ 131 (149)
.+++.++..+++|.|+|+|+....||..+
T Consensus 87 ~~~v~l~~~L~~G~YtV~Wrvvs~DGH~~ 115 (124)
T PRK10301 87 QLIVPLADSLKPGTYTVDWHVVSVDGHKT 115 (124)
T ss_pred EEEEECCCCCCCccEEEEEEEEecCCCcc
Confidence 35667777889999999999999998764
No 22
>smart00675 DM11 Domains in hypothetical proteins in Drosophila including 2 in CG15241 and CG9329.
Probab=92.50 E-value=3 Score=30.15 Aligned_cols=105 Identities=18% Similarity=0.184 Sum_probs=59.8
Q ss_pred ccceeeCCCCCC------ccEEEeEEEEeCCCCCCCCcEEEEEEEEeCeEeccc-EEEEEEE---E-CCEEecc----CC
Q 032005 20 AIGVKYCDKKKN------YAVTIQQVKIIPDPVVTGKPATFNISAVTGQAVYGG-KVVINVA---Y-FGVPVHQ----ET 84 (149)
Q Consensus 20 ~~~~~~C~~~~~------~~~~i~~~~i~Pc~~~~G~~~~i~~~~~~~~~i~~~-~~~v~~~---~-~gi~v~~----~~ 84 (149)
.--|++|.++.+ ..+.+++.++.. .+..++++...+..-+++-. .+++.+. + .|...|. ..
T Consensus 10 ~~ifs~C~n~~pg~~~i~~~~D~S~l~~~~----d~~~i~vsGn~t~~wdi~P~DrI~~~~~~~~~eRG~W~PTv~s~~~ 85 (164)
T smart00675 10 PDLYSPCTDAPPGNIGLREAFDISNLVVDM----DPDGLHISGNITVIWDVQPTDRISARVSVMHFERGTWQPTVFNMAT 85 (164)
T ss_pred ccccccCCCCCCCccchhhccchhheEEEE----cCCeEEEeeeEEEEEecCCCCeEEEEEEEEEecCCeeeeeEEeeec
Confidence 446889988643 245666777764 45566666666666677433 3333322 2 2333332 26
Q ss_pred cCCCCC-----------------------CCCCCCCCe-EE---EEEEEEc---CCCCCCeeEEEEEEEE--cCCC
Q 032005 85 RDVCEE-----------------------VSCPIAAGD-FV---LSHTQTL---PSFTPPGSYTLKMTME--DKNN 128 (149)
Q Consensus 85 ~d~C~~-----------------------~~CPl~~G~-~~---~~~~~~i---p~~~P~g~~~v~~~l~--d~~~ 128 (149)
.|.|.. -+||-.||. +. |...+.+ +...-.|+|.+.+++. |++|
T Consensus 86 ~dFC~~m~d~~q~WY~~wtk~i~N~~evk~kC~~~~Gtv~~~e~~~~~l~~~n~~~p~~~Gr~K~v~~~~AfD~~~ 161 (164)
T smart00675 86 PDFCKSMFDKNQYWYKYWTKYISNKEEIKEKCLTTKGTVLVYEPFLLKLKLSNVNGPNLRGRYKAVVTFEAFDEKN 161 (164)
T ss_pred cChhHHhcCCCcchHHHHHHhcccHHHHHhcCCCCCCeEEEecceeEEEEEeccCCCCcCCcEEEEEEEEeecccC
Confidence 899962 169999998 43 3334433 4334468886665554 5544
No 23
>PLN02991 oxidoreductase
Probab=91.48 E-value=0.9 Score=38.93 Aligned_cols=34 Identities=18% Similarity=0.455 Sum_probs=20.3
Q ss_pred EEECCEEeccC-CcCCCCCCCCCCCCCe-EEEEEEE
Q 032005 73 VAYFGVPVHQE-TRDVCEEVSCPIAAGD-FVLSHTQ 106 (149)
Q Consensus 73 ~~~~gi~v~~~-~~d~C~~~~CPl~~G~-~~~~~~~ 106 (149)
+.+-|+..+.. ..|.=-++.||++||+ |+|++..
T Consensus 83 iHWHGi~q~~~~~~DGv~~tQcpI~PG~sftY~F~~ 118 (543)
T PLN02991 83 ISWSGIRNWRNSYQDGVYGTTCPIPPGKNYTYALQV 118 (543)
T ss_pred EEECCcccCCCccccCCCCCCCccCCCCcEEEEEEe
Confidence 44556554221 2333224789999998 7777765
No 24
>PF05404 TRAP-delta: Translocon-associated protein, delta subunit precursor (TRAP-delta); InterPro: IPR008855 This family consists of several eukaryotic translocon-associated protein, delta subunit precursors (TRAP-delta or SSR-delta). The exact function of this protein is unknown [].; GO: 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=91.23 E-value=3 Score=30.21 Aligned_cols=102 Identities=14% Similarity=0.159 Sum_probs=48.1
Q ss_pred CcceehHHHHHHHhhhccCccceeeCCCCCCccEEEeEEEEeCCCCCCCCcEEEEEEEEeCeEecccEEEEEEEECCEEe
Q 032005 1 MDRQLMLFACFLLLVSSTQAIGVKYCDKKKNYAVTIQQVKIIPDPVVTGKPATFNISAVTGQAVYGGKVVINVAYFGVPV 80 (149)
Q Consensus 1 m~~~~~l~~~~~~~~~~~~~~~~~~C~~~~~~~~~i~~~~i~Pc~~~~G~~~~i~~~~~~~~~i~~~~~~v~~~~~gi~v 80 (149)
|.++ +++++++++.+.+ +.|.+. .++-+.-+-+-- ....++.+-++|++.=+=......+.+.++|..+
T Consensus 1 m~~~-~~~~~~~~~~~~~-----~~C~~P---~v~~ssytT~Da--~i~t~~afi~EFsl~C~n~~~~~~LyAeV~Gk~~ 69 (167)
T PF05404_consen 1 MKKI-VALLALLVSFCAA-----ETCENP---EVTSSSYTTTDA--TISTQTAFIAEFSLKCSNGAKNISLYAEVNGKIL 69 (167)
T ss_pred ChhH-HHHHHHHHHHhhc-----cccCCC---ceeeeeeecCCc--eeEeeeEEEEEEEEEeCCCCcCccEEEEECCEEE
Confidence 8887 3334344444433 578765 223222221111 2223333344444433211123456667777655
Q ss_pred ccCCcCCCCCCCCCCCCCe-EEEEEEEEcC-CCCCCeeEEEEEEEEcCC
Q 032005 81 HQETRDVCEEVSCPIAAGD-FVLSHTQTLP-SFTPPGSYTLKMTMEDKN 127 (149)
Q Consensus 81 ~~~~~d~C~~~~CPl~~G~-~~~~~~~~ip-~~~P~g~~~v~~~l~d~~ 127 (149)
|--.. |+ -.|+.+...+ +..++|+|.|++ +|++
T Consensus 70 PVar~------------~~~nkYQVSW~~e~k~a~sG~y~V~~--fDEe 104 (167)
T PF05404_consen 70 PVARS------------GDTNKYQVSWTEEHKKASSGTYEVKF--FDEE 104 (167)
T ss_pred EEEEc------------CCCCceEEEEEechhhccCCceEEEE--eChH
Confidence 53211 11 2455665555 667889888764 5554
No 25
>PF00339 Arrestin_N: Arrestin (or S-antigen), N-terminal domain; InterPro: IPR011021 G protein-coupled receptors are a large family of signalling molecules that respond to a wide variety of extracellular stimuli. The receptors relay the information encoded by the ligand through the activation of heterotrimeric G proteins and intracellular effector molecules. To ensure the appropriate regulation of the signalling cascade, it is vital to properly inactivate the receptor. This inactivation is achieved, in part, by the binding of a soluble protein, arrestin, which uncouples the receptor from the downstream G protein after the receptors are phosphorylated by G protein-coupled receptor kinases. In addition to the inactivation of G protein-coupled receptors, arrestins have also been implicated in the endocytosis of receptors and cross talk with other signalling pathways. Arrestin (retinal S-antigen) is a major protein of the retinal rod outer segments. It interacts with photo-activated phosphorylated rhodopsin, inhibiting or 'arresting' its ability to interact with transducin []. The protein binds calcium, and shows similarity in its C terminus to alpha-transducin and other purine nucleotide-binding proteins. In mammals, arrestin is associated with autoimmune uveitis. Arrestins comprise a family of closely-related proteins that includes beta-arrestin-1 and -2, which regulate the function of beta-adrenergic receptors by binding to their phosphorylated forms, impairing their capacity to activate G(S) proteins; Cone photoreceptors C-arrestin (arrestin-X) [], which could bind to phosphorylated red/green opsins; and Drosophila phosrestins I and II, which undergo light-induced phosphorylation, and probably play a role in photoreceptor transduction [, , ]. The crystal structure of bovine retinal arrestin comprises two domains of antiparallel beta-sheets connected through a hinge region and one short alpha-helix on the back of the amino-terminal fold []. The binding region for phosphorylated light-activated rhodopsin is located at the N-terminal domain, as indicated by the docking of the photoreceptor to the three-dimensional structure of arrestin. The N-terminal domain consists of an immunoglobulin-like beta-sandwich structure. This entry represents proteins with immunoglobulin-like domains that are similar to those found in arrestin.; PDB: 1SUJ_A 3UGX_A 1CF1_B 1AYR_A 3UGU_A 3P2D_B 1ZSH_A 2WTR_B 3GC3_A 1G4R_A ....
Probab=89.56 E-value=0.57 Score=32.13 Aligned_cols=32 Identities=28% Similarity=0.458 Sum_probs=17.4
Q ss_pred CCCCCCCeEEEEEEEEcCCCCCC--------eeEEEEEEE
Q 032005 92 SCPIAAGDFVLSHTQTLPSFTPP--------GSYTLKMTM 123 (149)
Q Consensus 92 ~CPl~~G~~~~~~~~~ip~~~P~--------g~~~v~~~l 123 (149)
..-+.+|+|+|.+++.+|..+|+ .+|.+++.+
T Consensus 87 ~~~l~~G~~~fpF~f~LP~~lP~S~~~~~g~I~Y~l~a~l 126 (149)
T PF00339_consen 87 PNILPPGEYEFPFEFQLPSNLPSSFEGSHGSIRYKLKATL 126 (149)
T ss_dssp -----C-TTEEEEEE---TTS--SEEEE-SEEEEEEEEEE
T ss_pred eecccCCCEEEEEEEECCCCCCceEeccCcCEEEEEEEEE
Confidence 45688999999999999988776 467777777
No 26
>PLN02168 copper ion binding / pectinesterase
Probab=88.03 E-value=2.7 Score=36.10 Aligned_cols=54 Identities=15% Similarity=0.276 Sum_probs=29.5
Q ss_pred CCCCCcEEEEEEEEeCeEecccEEEEEEEECCEEeccC-CcCCCCCCCCCCCCCe-EEEEEEE
Q 032005 46 VVTGKPATFNISAVTGQAVYGGKVVINVAYFGVPVHQE-TRDVCEEVSCPIAAGD-FVLSHTQ 106 (149)
Q Consensus 46 ~~~G~~~~i~~~~~~~~~i~~~~~~v~~~~~gi~v~~~-~~d~C~~~~CPl~~G~-~~~~~~~ 106 (149)
.++|+++.|++.=.+++ . ..+.+-|+..+.. ..|.=-++.||++||+ |+|.++.
T Consensus 61 ~~~GD~v~V~v~N~L~~----~---ttiHWHGl~~~~~~~~DGv~gtQcpI~PG~sftY~F~~ 116 (545)
T PLN02168 61 ATANDVINVNIFNNLTE----P---FLMTWNGLQLRKNSWQDGVRGTNCPILPGTNWTYRFQV 116 (545)
T ss_pred EECCCEEEEEEEeCCCC----C---ccEeeCCccCCCCCCcCCCCCCcCCCCCCCcEEEEEEe
Confidence 45566666655433321 1 1345556555433 1232223789999998 7777665
No 27
>PLN02354 copper ion binding / oxidoreductase
Probab=87.88 E-value=2.1 Score=36.73 Aligned_cols=17 Identities=29% Similarity=0.724 Sum_probs=13.5
Q ss_pred CCCCCCCCCe-EEEEEEE
Q 032005 90 EVSCPIAAGD-FVLSHTQ 106 (149)
Q Consensus 90 ~~~CPl~~G~-~~~~~~~ 106 (149)
++.||+.||+ |+|.++.
T Consensus 100 ~TQcpI~PG~sf~Y~F~~ 117 (552)
T PLN02354 100 GTNCPIPPGTNFTYHFQP 117 (552)
T ss_pred CCcCCCCCCCcEEEEEEe
Confidence 3789999998 7777763
No 28
>KOG3205 consensus Rho GDP-dissociation inhibitor [Signal transduction mechanisms]
Probab=87.62 E-value=9.5 Score=28.21 Aligned_cols=92 Identities=18% Similarity=0.230 Sum_probs=55.5
Q ss_pred CCCCCcEEEEEEEEeCeEeccc-EEEEEEEECCEEeccCCcCCCCCCCCCCCCCeEEEEEEEEc---C-CCCCCeeEEEE
Q 032005 46 VVTGKPATFNISAVTGQAVYGG-KVVINVAYFGVPVHQETRDVCEEVSCPIAAGDFVLSHTQTL---P-SFTPPGSYTLK 120 (149)
Q Consensus 46 ~~~G~~~~i~~~~~~~~~i~~~-~~~v~~~~~gi~v~~~~~d~C~~~~CPl~~G~~~~~~~~~i---p-~~~P~g~~~v~ 120 (149)
++.|..+.+.+.|..+++|-+| ...-.+.--|+.+-...+=+ |. ..|..-.|.+..+. | ..+-.|+|.++
T Consensus 101 iKEGs~Y~lki~F~Vq~eIvSGLrY~q~v~r~Gv~VDk~~~Ml--GS---y~P~~e~ye~~~p~eeAPsGmlaRG~Ys~~ 175 (200)
T KOG3205|consen 101 IKEGSEYRLKISFRVQREIVSGLRYVQTVYRTGVKVDKTKYML--GS---YGPQAEPYEFVTPEEEAPSGMLARGSYSAK 175 (200)
T ss_pred eecCcEEEEEEEEEEeeheeccceeeeEEeecceEEeehhhhc--cc---CCCCCcceeeeCCcccCCccceeecceeee
Confidence 6889999999999999998888 43334444567664332211 12 12222122222221 1 23445799999
Q ss_pred EEEEcCCCCEEEEEEEEEEEcc
Q 032005 121 MTMEDKNNEELTCFSFNFKIGF 142 (149)
Q Consensus 121 ~~l~d~~~~~~~C~~~~v~i~~ 142 (149)
-.+.|+|+..-.=.+-.+.|..
T Consensus 176 skF~DDDk~~hLe~~w~~~I~K 197 (200)
T KOG3205|consen 176 SKFTDDDKTCHLEWNWTFDIKK 197 (200)
T ss_pred eEEecCCCceEEEEEEEEEEee
Confidence 9999988765555566666654
No 29
>PF03443 Glyco_hydro_61: Glycosyl hydrolase family 61; InterPro: IPR005103 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The only known activity within this family is that of endoglucanase (3.2.1.4 from EC) GH61 from CAZY ; PDB: 4EIS_B 2VTC_A 4EIR_B 3EJA_D 3EII_A.
Probab=87.17 E-value=2.5 Score=31.91 Aligned_cols=40 Identities=28% Similarity=0.440 Sum_probs=27.9
Q ss_pred EEEEEEcCCCCCCeeEEEEEEEEcCC------CCE--EEEEEEEEEEc
Q 032005 102 LSHTQTLPSFTPPGSYTLKMTMEDKN------NEE--LTCFSFNFKIG 141 (149)
Q Consensus 102 ~~~~~~ip~~~P~g~~~v~~~l~d~~------~~~--~~C~~~~v~i~ 141 (149)
-+.++.||+.+|+|+|-+|.|+..=+ +.+ ..|+++.|+=.
T Consensus 136 ~~~~~~IP~~l~~G~YLlR~E~IaLH~a~~~~gaQfY~~Caqi~Vtg~ 183 (218)
T PF03443_consen 136 GSWTFTIPKNLPPGQYLLRHEIIALHSAGQPGGAQFYPSCAQIKVTGG 183 (218)
T ss_dssp CEEEEE--TTBBSEEEEEEEEEEE-TTTTSTT--EEEEEEEEEEEESS
T ss_pred CceEEEeCCCCCCCCceEEecceeeccCccCCCCEEhhhCEEEEEECC
Confidence 36677899999999999998888522 445 68999888643
No 30
>TIGR02186 alph_Pro_TM conserved hypothetical protein. This family consists of predicted transmembrane proteins of about 270 amino acids. Members are found, so far, only among the Alphaproteobacteria and only once in each genome.
Probab=86.49 E-value=3.3 Score=32.20 Aligned_cols=41 Identities=15% Similarity=0.186 Sum_probs=35.5
Q ss_pred EEEEEEEcCCCCCCeeEEEEEEEEcCCCCEEEEEEEEEEEcc
Q 032005 101 VLSHTQTLPSFTPPGSYTLKMTMEDKNNEELTCFSFNFKIGF 142 (149)
Q Consensus 101 ~~~~~~~ip~~~P~g~~~v~~~l~d~~~~~~~C~~~~v~i~~ 142 (149)
-|..++.+|..+|.|.|+++..+.- +|+.+.=.+.++.+.+
T Consensus 181 LFra~i~LPAnvp~G~Y~v~v~L~r-~G~vv~~~~t~l~V~K 221 (261)
T TIGR02186 181 LFRATLRLPANVPNGTHEVRAYLFR-GGVFIARTELALEIVK 221 (261)
T ss_pred eEEEeeecCCCCCCceEEEEEEEEe-CCEEEEEEEeEEEEEE
Confidence 3677888999999999999999984 5888988888888876
No 31
>PF09608 Alph_Pro_TM: Putative transmembrane protein (Alph_Pro_TM); InterPro: IPR019088 This entry consists of predicted transmembrane proteins of about 270 amino acids. They are found predominantly, though not exclusively, in alphaproteobacteria, generally only once in each genome.
Probab=84.77 E-value=4.6 Score=30.91 Aligned_cols=41 Identities=17% Similarity=0.397 Sum_probs=34.2
Q ss_pred EEEEEEEcCCCCCCeeEEEEEEEEcCCCCEEEEEEEEEEEcc
Q 032005 101 VLSHTQTLPSFTPPGSYTLKMTMEDKNNEELTCFSFNFKIGF 142 (149)
Q Consensus 101 ~~~~~~~ip~~~P~g~~~v~~~l~d~~~~~~~C~~~~v~i~~ 142 (149)
-|..++.+|...|.|.|+++.-+.- ||+.+.=.+-++++.+
T Consensus 156 lFra~i~LPanvp~G~Y~v~v~l~r-dG~vv~~~~~~l~V~K 196 (236)
T PF09608_consen 156 LFRARIPLPANVPPGDYTVRVYLFR-DGQVVASQETPLRVRK 196 (236)
T ss_pred eEEEEeEcCCCCCcceEEEEEEEEE-CCEEEEEEeeEEEEEE
Confidence 4678899999999999999999985 5878877777777765
No 32
>cd00918 Der-p2_like Several group 2 allergen proteins belong to the ML domain family. They include Dermatophagoides pteronyssinus, group 2 (Der p 2) and D. farinae, group 2 (Der f 2) allergens. These house dust mites cause heavy atopic diseases such as asthma and dermatitis. Although the allergenic properties of these proteins have been well characterized, their biological function in mites is unknown.
Probab=84.66 E-value=2.2 Score=29.19 Aligned_cols=34 Identities=12% Similarity=0.092 Sum_probs=27.1
Q ss_pred CCCCCCCCcEEEEEEEEeCeEecccEEEEEEEEC
Q 032005 43 PDPVVTGKPATFNISAVTGQAVYGGKVVINVAYF 76 (149)
Q Consensus 43 Pc~~~~G~~~~i~~~~~~~~~i~~~~~~v~~~~~ 76 (149)
-||+++|+.++.+.++.........++++++.+.
T Consensus 72 ~CPl~~G~~~~y~~~~~V~~~~P~v~~~V~~~L~ 105 (120)
T cd00918 72 KCPIKKGQHYDIKYTWNVPAILPKIKAVVKAVLI 105 (120)
T ss_pred eCCCcCCcEEEEEEeeeccccCCCeEEEEEEEEE
Confidence 4999999999999999887766666666666554
No 33
>cd00912 ML The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2 and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids.
Probab=84.01 E-value=3.4 Score=28.09 Aligned_cols=40 Identities=25% Similarity=0.316 Sum_probs=31.3
Q ss_pred CcCCCCCCCCCCCCCe-EEEEEEEEcCCCCCCeeEEEEEEE
Q 032005 84 TRDVCEEVSCPIAAGD-FVLSHTQTLPSFTPPGSYTLKMTM 123 (149)
Q Consensus 84 ~~d~C~~~~CPl~~G~-~~~~~~~~ip~~~P~g~~~v~~~l 123 (149)
....|+..+||+..|+ .+.+.++........++..+.+++
T Consensus 15 ~v~pc~~~pC~~~~g~~~~i~~~f~~~~~~~~~~~~v~~~~ 55 (127)
T cd00912 15 LLSPCDPLPCPDHRGGNYNLSVTGTLREDIKSLYVDLALMS 55 (127)
T ss_pred EeCCCCCCCCcccCCCeEEEEEEEEECccccEEEEEEEEEE
Confidence 3466888899999998 788888888877777777666654
No 34
>PF13002 LDB19: Arrestin_N terminal like; InterPro: IPR024391 This entry represents a predicted Ig-like beta sandwich domain found towards the N terminus of protein LDB19 []. It is also found in other sequences and is related to the arrestin N-terminal fold [].
Probab=83.81 E-value=4.8 Score=29.84 Aligned_cols=52 Identities=13% Similarity=0.234 Sum_probs=38.3
Q ss_pred CCCCCCCeEEEEEEEEcCCCCCC-----------eeEEEEEEEEcCC-------C-CEEEEEEEEEEEccc
Q 032005 92 SCPIAAGDFVLSHTQTLPSFTPP-----------GSYTLKMTMEDKN-------N-EELTCFSFNFKIGFH 143 (149)
Q Consensus 92 ~CPl~~G~~~~~~~~~ip~~~P~-----------g~~~v~~~l~d~~-------~-~~~~C~~~~v~i~~~ 143 (149)
+..+.+|.+.|.++..||..+|. ++|.+.++....+ + .....++-++.|.|+
T Consensus 44 ~t~l~~G~h~fPFS~LiPG~LPaS~~lgs~~l~~I~Yel~A~a~~~~~~~~~~~~~~~~~~~~~pl~V~Rs 114 (191)
T PF13002_consen 44 PTTLTKGSHAFPFSYLIPGHLPASMDLGSTPLVSIKYELKAEATYKDPRRGSSSSKPRVLKLKRPLPVKRS 114 (191)
T ss_pred ccccCCCcccCCeeEECCCCCccccccCCCCcEEEEEEEEEEEEEccCccccCCCcceeEEEeeeEEEEEe
Confidence 67899999999999999877665 3566666666521 2 345789999999883
No 35
>PF07495 Y_Y_Y: Y_Y_Y domain; InterPro: IPR011123 This region is mostly found at the end of the beta propellers (IPR011110 from INTERPRO) in a family of two component regulators. However they are also found tandemly repeated in Q891H4 from SWISSPROT without other signal conduction domains being present. It is named after the conserved tyrosines found in the alignment. The exact function is not known.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
Probab=83.40 E-value=1.7 Score=25.69 Aligned_cols=29 Identities=34% Similarity=0.530 Sum_probs=17.9
Q ss_pred CCCeeEEEEEEEEcCCCCE-EEEEEEEEEE
Q 032005 112 TPPGSYTLKMTMEDKNNEE-LTCFSFNFKI 140 (149)
Q Consensus 112 ~P~g~~~v~~~l~d~~~~~-~~C~~~~v~i 140 (149)
+|+|+|+++++.+|.+++. .....+.++|
T Consensus 36 L~~G~Y~l~V~a~~~~~~~~~~~~~l~i~I 65 (66)
T PF07495_consen 36 LPPGKYTLEVRAKDNNGKWSSDEKSLTITI 65 (66)
T ss_dssp --SEEEEEEEEEEETTS-B-SS-EEEEEEE
T ss_pred CCCEEEEEEEEEECCCCCcCcccEEEEEEE
Confidence 6899999999999987643 2224444444
No 36
>smart00737 ML Domain involved in innate immunity and lipid metabolism. ML (MD-2-related lipid-recognition) is a novel domain identified in MD-1, MD-2, GM2A, Npc2 and multiple proteins of unknown function in plants, animals and fungi. These single-domain proteins were predicted to form a beta-rich fold containing multiple strands, and to mediate diverse biological functions through interacting with specific lipids.
Probab=83.18 E-value=3 Score=27.82 Aligned_cols=33 Identities=15% Similarity=0.198 Sum_probs=27.3
Q ss_pred CCCCCCCCcEEEEEEEEeCeEecccEEEEEEEE
Q 032005 43 PDPVVTGKPATFNISAVTGQAVYGGKVVINVAY 75 (149)
Q Consensus 43 Pc~~~~G~~~~i~~~~~~~~~i~~~~~~v~~~~ 75 (149)
.||+.+|+.+..+..+..+..+..+++.+.+.+
T Consensus 71 ~CPl~~G~~~~~~~~~~v~~~~P~~~~~v~~~l 103 (118)
T smart00737 71 KCPIEKGETVNYTNSLTVPGIFPPGKYTVKWEL 103 (118)
T ss_pred CCCCCCCeeEEEEEeeEccccCCCeEEEEEEEE
Confidence 699999999999999888887777777665554
No 37
>PF02221 E1_DerP2_DerF2: ML domain; InterPro: IPR003172 The MD-2-related lipid-recognition (ML) domain is implicated in lipid recognition, particularly in the recognition of pathogen related products. It has an immunoglobulin-like beta-sandwich fold similar to that of E-set Ig domains. This domain is present in the following proteins: Epididymal secretory protein E1 (also known as Niemann-Pick C2 protein), which is known to bind cholesterol. Niemann-Pick disease type C2 is a fatal hereditary disease characterised by accumulation of low-density lipoprotein-derived cholesterol in lysosomes []. House-dust mite allergen proteins such as Der f 2 from Dermatophagoides farinae and Der p 2 from Dermatophagoides pteronyssinus []. ; PDB: 2AG9_B 1G13_B 2AG2_B 2AG4_A 1TJJ_C 1PU5_C 1PUB_A 2AF9_A 3T6Q_D 3M7O_B ....
Probab=82.80 E-value=2.4 Score=28.68 Aligned_cols=34 Identities=18% Similarity=0.212 Sum_probs=28.1
Q ss_pred eCCCCCCCCcEEEEEEEEeCeEecccEEEEEEEE
Q 032005 42 IPDPVVTGKPATFNISAVTGQAVYGGKVVINVAY 75 (149)
Q Consensus 42 ~Pc~~~~G~~~~i~~~~~~~~~i~~~~~~v~~~~ 75 (149)
.+||+++|+.++.+.++..+.....++..+.+.+
T Consensus 84 ~~CPi~~G~~~~~~~~~~i~~~~p~~~~~i~~~l 117 (134)
T PF02221_consen 84 LSCPIKAGEYYTYTYTIPIPKIYPPGKYTIQWKL 117 (134)
T ss_dssp TTSTBTTTEEEEEEEEEEESTTSSSEEEEEEEEE
T ss_pred ccCccCCCcEEEEEEEEEcccceeeEEEEEEEEE
Confidence 4899999999999999999988877877665544
No 38
>PF00868 Transglut_N: Transglutaminase family; InterPro: IPR001102 Synonym(s): Protein-glutamine gamma-glutamyltransferase, Fibrinoligase, TGase Protein-glutamine gamma-glutamyltransferases (2.3.2.13 from EC) (TGase) are calcium-dependent enzymes that catalyse the cross-linking of proteins by promoting the formation of isopeptide bonds between the gamma-carboxyl group of a glutamine in one polypeptide chain and the epsilon-amino group of a lysine in a second polypeptide chain. TGases also catalyse the conjugation of polyamines to proteins [, ]. Transglutaminases are widely distributed in various organs, tissues and body fluids. The best known transglutaminase is blood coagulation factor XIII, a plasma tetrameric protein composed of two catalytic A subunits and two non-catalytic B subunits. Factor XIII is responsible for cross-linking fibrin chains, thus stabilising the fibrin clot. There are commonly three domains: N-terminal, middle (IPR013808 from INTERPRO) and C-terminal (IPR013807 from INTERPRO). This entry represents the N-terminal domain found in transglutaminases.; GO: 0018149 peptide cross-linking; PDB: 1L9N_B 1NUF_A 1NUD_A 1NUG_B 1L9M_A 1KV3_C 3S3S_A 2Q3Z_A 3LY6_A 3S3P_A ....
Probab=82.24 E-value=6.9 Score=26.52 Aligned_cols=78 Identities=17% Similarity=0.201 Sum_probs=40.6
Q ss_pred CCCCCcEEEEEEEEeCeEecccEEEEEEEECCEEeccCCcCCCC-CCCCCCCCCe----------EEEEEEEEcCCCCCC
Q 032005 46 VVTGKPATFNISAVTGQAVYGGKVVINVAYFGVPVHQETRDVCE-EVSCPIAAGD----------FVLSHTQTLPSFTPP 114 (149)
Q Consensus 46 ~~~G~~~~i~~~~~~~~~i~~~~~~v~~~~~gi~v~~~~~d~C~-~~~CPl~~G~----------~~~~~~~~ip~~~P~ 114 (149)
+.||+...|.+.|.-..+-..-.+.+....|..+-... .-... .......++. -..+..+..|...|-
T Consensus 29 VRRGQ~F~i~l~f~r~~~~~~d~l~l~~~~G~~P~~~~-gT~~~~~~~~~~~~~~W~a~v~~~~~~~~tv~V~spa~A~V 107 (118)
T PF00868_consen 29 VRRGQPFTITLRFNRPFDPSKDQLSLEFETGPNPSESK-GTKVVFPVSSSLDSSSWSARVESQDGNSVTVSVTSPANAPV 107 (118)
T ss_dssp EETTSEEEEEEEESSS--TTTEEEEEEEEESSS--TTT-TSEEEEEECSSS-TSSSEEEEEEEETTEEEEEEE--TTS--
T ss_pred EECCCEEEEEEEEcCCcCCCCcEEEEEEEEecccccCC-CcEEEEEEccCCCCCCEEEEEEecCCCEEEEEEECCCCCce
Confidence 68999999999998885444446777777773211000 00000 0011111111 235666778888899
Q ss_pred eeEEEEEEEE
Q 032005 115 GSYTLKMTME 124 (149)
Q Consensus 115 g~~~v~~~l~ 124 (149)
|+|.+.+...
T Consensus 108 G~y~l~v~~~ 117 (118)
T PF00868_consen 108 GRYKLSVETK 117 (118)
T ss_dssp EEEEEEEEEE
T ss_pred EEEEEEEEEe
Confidence 9998887653
No 39
>PLN02835 oxidoreductase
Probab=81.68 E-value=7.5 Score=33.35 Aligned_cols=34 Identities=15% Similarity=0.397 Sum_probs=19.9
Q ss_pred EEECCEEeccC-CcCCCCCCCCCCCCCe-EEEEEEE
Q 032005 73 VAYFGVPVHQE-TRDVCEEVSCPIAAGD-FVLSHTQ 106 (149)
Q Consensus 73 ~~~~gi~v~~~-~~d~C~~~~CPl~~G~-~~~~~~~ 106 (149)
+.+-|+..+.. ..|.=-++.||++||+ |+|++..
T Consensus 84 iHWHGl~~~~~~~~DGv~~tQ~pI~PG~sf~Y~F~~ 119 (539)
T PLN02835 84 LTWNGIKQRKNSWQDGVLGTNCPIPPNSNYTYKFQT 119 (539)
T ss_pred EEeCCcccCCCCCCCCCccCcCCCCCCCcEEEEEEE
Confidence 44555555432 2232223789999998 6766653
No 40
>PF12988 DUF3872: Domain of unknown function, B. Theta Gene description (DUF3872); InterPro: IPR024355 This entry represents proteins of unknown function found primarily in Bacteroides species. The Bacteroides thetaiotaomicron gene coding for this protein is located in a conjugate transposon and appears to be upregulated in the presence of host or other bacterial species compared to growth in pure culture [, ].; PDB: 2L3B_A 2L7Q_A.
Probab=81.36 E-value=4.1 Score=28.48 Aligned_cols=100 Identities=17% Similarity=0.198 Sum_probs=40.3
Q ss_pred ceeeCCCCC----CccEEEeEEEEeCC--CCCCCCcEEEEEEEEeCeEecccEEEEE-EEECCE-EeccCCcCCCCC-CC
Q 032005 22 GVKYCDKKK----NYAVTIQQVKIIPD--PVVTGKPATFNISAVTGQAVYGGKVVIN-VAYFGV-PVHQETRDVCEE-VS 92 (149)
Q Consensus 22 ~~~~C~~~~----~~~~~i~~~~i~Pc--~~~~G~~~~i~~~~~~~~~i~~~~~~v~-~~~~gi-~v~~~~~d~C~~-~~ 92 (149)
-+..|++.- .+.++ ++..|- .+++|+++.|+....-..+.......+. ....|- .+-..+.-.... -.
T Consensus 17 ~l~sC~deLDIQQ~YpF~---v~tmPVpk~I~~GeTvEIR~~l~reG~y~~t~Y~iRYFQ~dGkG~L~~~~g~~~~pND~ 93 (137)
T PF12988_consen 17 LLSSCDDELDIQQAYPFT---VETMPVPKKIKKGETVEIRCELKREGNYADTRYTIRYFQPDGKGTLRMDDGTVLLPNDR 93 (137)
T ss_dssp ------TTS------SEE---EEE----SS--TTEEEEEEEEEEESS--SS---EEEEE-SSS-EEEEETTS-EE-TTSE
T ss_pred HHhhcCCccceeecCCcE---EEEeccccccCCCCEEEEEEEEecCceecccEEEEEEEeecCCEEEEecCCcEeccccc
Confidence 456787652 24553 344444 4899999999999988887766554443 223331 111111111110 12
Q ss_pred CCCCCCeEEEEEEEEcCCCCCCeeEEEEEEEEcCCCC
Q 032005 93 CPIAAGDFVLSHTQTLPSFTPPGSYTLKMTMEDKNNE 129 (149)
Q Consensus 93 CPl~~G~~~~~~~~~ip~~~P~g~~~v~~~l~d~~~~ 129 (149)
=|++++++.+.++-.= ...=++.+.+.|.-|+
T Consensus 94 Y~L~~~~FRLYYTS~s-----~~~q~idv~veDnfGq 125 (137)
T PF12988_consen 94 YPLEKEVFRLYYTSRS-----DDQQTIDVYVEDNFGQ 125 (137)
T ss_dssp EE-S-SEEEEEEEE-S-----SS-EEEEEEEEETTTE
T ss_pred eecCcCEEEEEEecCC-----CCCceeEEEEEeCCCC
Confidence 3577777655444321 3345667777776663
No 41
>KOG1263 consensus Multicopper oxidases [Secondary metabolites biosynthesis, transport and catabolism]
Probab=81.14 E-value=4.5 Score=34.94 Aligned_cols=34 Identities=26% Similarity=0.499 Sum_probs=20.6
Q ss_pred EEECCEEecc-CCcCCCCC-CCCCCCCCe-EEEEEEEE
Q 032005 73 VAYFGVPVHQ-ETRDVCEE-VSCPIAAGD-FVLSHTQT 107 (149)
Q Consensus 73 ~~~~gi~v~~-~~~d~C~~-~~CPl~~G~-~~~~~~~~ 107 (149)
+.+.|+.-.. .-.|. .. +.||++||+ |+|.+++.
T Consensus 83 ihWhGv~q~kn~w~DG-~~~TqCPI~Pg~~~tY~F~v~ 119 (563)
T KOG1263|consen 83 IHWHGVRQRKNPWQDG-VYITQCPIQPGENFTYRFTVK 119 (563)
T ss_pred EEeccccccCCccccC-CccccCCcCCCCeEEEEEEeC
Confidence 4455543221 13466 43 799999998 77766654
No 42
>COG2372 CopC Uncharacterized protein, homolog of Cu resistance protein CopC [General function prediction only]
Probab=80.66 E-value=6.8 Score=27.13 Aligned_cols=29 Identities=17% Similarity=0.271 Sum_probs=25.1
Q ss_pred EEEEEcCCCCCCeeEEEEEEEEcCCCCEE
Q 032005 103 SHTQTLPSFTPPGSYTLKMTMEDKNNEEL 131 (149)
Q Consensus 103 ~~~~~ip~~~P~g~~~v~~~l~d~~~~~~ 131 (149)
.+.++++..+..|.|++.|+....||...
T Consensus 88 ~l~v~l~~~L~aG~Y~v~WrvvS~DGH~v 116 (127)
T COG2372 88 QLEVPLPQPLKAGVYTVDWRVVSSDGHVV 116 (127)
T ss_pred EEEecCcccCCCCcEEEEEEEEecCCcEe
Confidence 56778889999999999999999988653
No 43
>PF13956 Ibs_toxin: Toxin Ibs, type I toxin-antitoxin system
Probab=80.07 E-value=1.3 Score=19.94 Aligned_cols=13 Identities=23% Similarity=0.554 Sum_probs=7.8
Q ss_pred CcceehHHHHHHH
Q 032005 1 MDRQLMLFACFLL 13 (149)
Q Consensus 1 m~~~~~l~~~~~~ 13 (149)
|.|++++++.+++
T Consensus 1 MMk~vIIlvvLLl 13 (19)
T PF13956_consen 1 MMKLVIILVVLLL 13 (19)
T ss_pred CceehHHHHHHHh
Confidence 7887666554333
No 44
>cd00916 Npc2_like Niemann-Pick type C2 (Npc2) is a lysosomal protein in which a mutation in the gene causes a rare form of Niemann-Pick type C disease, an autosomal recessive lipid storage disorder characterized by accumulation of low-density lipoprotein-derived cholesterol in lysosomes. Although Npc2 is known to bind cholesterol, the function of this protein is unknown. These proteins belong to the ML domain family.
Probab=79.77 E-value=4.2 Score=27.72 Aligned_cols=35 Identities=17% Similarity=0.185 Sum_probs=27.0
Q ss_pred eCCCCCCCCcEEEEEEEEeCeEecccEEEEEEEEC
Q 032005 42 IPDPVVTGKPATFNISAVTGQAVYGGKVVINVAYF 76 (149)
Q Consensus 42 ~Pc~~~~G~~~~i~~~~~~~~~i~~~~~~v~~~~~ 76 (149)
..||+++|+.++.+.++.........++++++.+.
T Consensus 75 ~~CPl~~G~~~~y~~~~~v~~~~P~i~~~v~~~L~ 109 (123)
T cd00916 75 TSCPLSAGEDVTYTLSLPVLAPYPGISVTVEWELT 109 (123)
T ss_pred CCCCCcCCcEEEEEEeeeccccCCCeEEEEEEEEE
Confidence 56999999999999988887766666666655543
No 45
>PF12984 DUF3868: Domain of unknown function, B. Theta Gene description (DUF3868); InterPro: IPR024480 This domain of unknown function is found in a number of bacterial proteins. The function of the proteins is not known, but the Bacteroides thetaiotaomicron gene appears to be upregulated in the presence of host or other bacterial species compared to pure culture [, ].
Probab=79.30 E-value=10 Score=25.57 Aligned_cols=31 Identities=10% Similarity=0.178 Sum_probs=24.0
Q ss_pred cEEEeEEEEeCCCCCCCCcEEEEEEEEeCe-Eeccc
Q 032005 33 AVTIQQVKIIPDPVVTGKPATFNISAVTGQ-AVYGG 67 (149)
Q Consensus 33 ~~~i~~~~i~Pc~~~~G~~~~i~~~~~~~~-~i~~~ 67 (149)
.++|++.++. +.|..+.|++++..+. ++.+.
T Consensus 29 ~i~v~~~~~~----~~gd~L~V~m~idl~~l~v~s~ 60 (115)
T PF12984_consen 29 QIKVTNVSVE----KQGDSLHVDMDIDLSGLKVKSN 60 (115)
T ss_pred cEEEEeeEEE----EECCEEEEEEEEEecccccCCC
Confidence 6788888876 6899999999988875 55544
No 46
>COG2967 ApaG Uncharacterized protein affecting Mg2+/Co2+ transport [Inorganic ion transport and metabolism]
Probab=77.16 E-value=4.8 Score=27.57 Aligned_cols=35 Identities=23% Similarity=0.378 Sum_probs=27.6
Q ss_pred CCCCe-EEEEEEEEcCCCCCCeeEEEEEEEEcCCCCEE
Q 032005 95 IAAGD-FVLSHTQTLPSFTPPGSYTLKMTMEDKNNEEL 131 (149)
Q Consensus 95 l~~G~-~~~~~~~~ip~~~P~g~~~v~~~l~d~~~~~~ 131 (149)
++||+ |+|+.--. -..|.|....+..+.|++|+.+
T Consensus 75 l~PG~~y~YtSg~~--l~Tp~G~M~GhY~M~~e~G~~F 110 (126)
T COG2967 75 LAPGEEYQYTSGCP--LDTPSGTMQGHYEMIDEDGETF 110 (126)
T ss_pred cCCCCceEEcCCcC--ccCCcceEEEEEEEecCCCcEE
Confidence 68887 77655444 4478999999999999999765
No 47
>PRK05461 apaG CO2+/MG2+ efflux protein ApaG; Reviewed
Probab=77.11 E-value=8.9 Score=26.51 Aligned_cols=49 Identities=24% Similarity=0.428 Sum_probs=33.8
Q ss_pred CCC-CCCCe-EEEEEEEEcCCCCCCeeEEEEEEEEcCCCCEEEEEEEEEEEcc
Q 032005 92 SCP-IAAGD-FVLSHTQTLPSFTPPGSYTLKMTMEDKNNEELTCFSFNFKIGF 142 (149)
Q Consensus 92 ~CP-l~~G~-~~~~~~~~ip~~~P~g~~~v~~~l~d~~~~~~~C~~~~v~i~~ 142 (149)
..| |+||+ |+|+....+. .|.|.....+.+.+++|+.+-+---+|.+..
T Consensus 72 ~qP~L~PGe~F~Y~S~~~l~--tp~G~M~G~y~~~~~~G~~F~v~Ip~F~L~~ 122 (127)
T PRK05461 72 EQPVLAPGESFEYTSGAVLE--TPSGTMQGHYQMVDEDGERFEVPIPPFRLAV 122 (127)
T ss_pred CCceECCCCCeEEeCCCCcc--CCCEEEEEEEEEEeCCCCEEEEEccCEEcCC
Confidence 455 47898 6665555554 6889999999999988987655554454443
No 48
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) [] are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2B39_B 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 4ACQ_C 2P9R_B ....
Probab=75.91 E-value=18 Score=23.10 Aligned_cols=72 Identities=19% Similarity=0.303 Sum_probs=35.1
Q ss_pred CCCCcEEEEEEEEeCe----EecccEEEEEEEE-CCEEeccCCcCCCCCCCCCCCCCeEEEEEEEEcCCCCCCeeEEEEE
Q 032005 47 VTGKPATFNISAVTGQ----AVYGGKVVINVAY-FGVPVHQETRDVCEEVSCPIAAGDFVLSHTQTLPSFTPPGSYTLKM 121 (149)
Q Consensus 47 ~~G~~~~i~~~~~~~~----~i~~~~~~v~~~~-~gi~v~~~~~d~C~~~~CPl~~G~~~~~~~~~ip~~~P~g~~~v~~ 121 (149)
+.|+++.+++...... ......+.+.+.- .|..+-.... .. .-..| .++.++.+|+..+.|.|++++
T Consensus 12 rPGetV~~~~~~~~~~~~~~~~~~~~~~v~i~dp~g~~v~~~~~---~~---~~~~G--~~~~~~~lp~~~~~G~y~i~~ 83 (99)
T PF01835_consen 12 RPGETVHFRAIVRDLDNDFKPPANSPVTVTIKDPSGNEVFRWSV---NT---TNENG--IFSGSFQLPDDAPLGTYTIRV 83 (99)
T ss_dssp -TTSEEEEEEEEEEECTTCSCESSEEEEEEEEETTSEEEEEEEE---EE---TTCTT--EEEEEEE--SS---EEEEEEE
T ss_pred CCCCEEEEEEEEeccccccccccCCceEEEEECCCCCEEEEEEe---ee---eCCCC--EEEEEEECCCCCCCEeEEEEE
Confidence 5788888887643333 1222334444433 2333211111 00 01234 356668999999999999999
Q ss_pred EEEcC
Q 032005 122 TMEDK 126 (149)
Q Consensus 122 ~l~d~ 126 (149)
...++
T Consensus 84 ~~~~~ 88 (99)
T PF01835_consen 84 KTDDD 88 (99)
T ss_dssp EETTT
T ss_pred EEccC
Confidence 99644
No 49
>PLN02604 oxidoreductase
Probab=75.72 E-value=14 Score=31.84 Aligned_cols=16 Identities=31% Similarity=0.777 Sum_probs=12.4
Q ss_pred CCCCCCCCe-EEEEEEE
Q 032005 91 VSCPIAAGD-FVLSHTQ 106 (149)
Q Consensus 91 ~~CPl~~G~-~~~~~~~ 106 (149)
..||+.||+ ++|.+..
T Consensus 100 tq~~i~pg~s~~y~f~~ 116 (566)
T PLN02604 100 TQCPILPGETFTYEFVV 116 (566)
T ss_pred ccCccCCCCeEEEEEEc
Confidence 579999998 6666653
No 50
>PF13752 DUF4165: Domain of unknown function (DUF4165)
Probab=75.63 E-value=21 Score=24.58 Aligned_cols=44 Identities=27% Similarity=0.492 Sum_probs=34.8
Q ss_pred CeEEEEEEEEcCCCCCCeeEEEEEEEEcCCCCEEEEEEEEEEEcc
Q 032005 98 GDFVLSHTQTLPSFTPPGSYTLKMTMEDKNNEELTCFSFNFKIGF 142 (149)
Q Consensus 98 G~~~~~~~~~ip~~~P~g~~~v~~~l~d~~~~~~~C~~~~v~i~~ 142 (149)
|.-.|-.++.+|+. ..|.|+++.++.|.+|..+.=-.-++.|..
T Consensus 78 G~efYGk~ltlp~l-~dG~ytvk~eiL~s~g~vV~t~s~~~~IDt 121 (124)
T PF13752_consen 78 GKEFYGKELTLPAL-GDGTYTVKSEILDSQGTVVQTYSYPFTIDT 121 (124)
T ss_pred CceeeeeEEEeccC-CCCcEEEEEEeeccCCCEEEeeeEeEEEec
Confidence 55445667778775 789999999999999988887777777754
No 51
>COG1470 Predicted membrane protein [Function unknown]
Probab=75.12 E-value=42 Score=28.52 Aligned_cols=32 Identities=25% Similarity=0.452 Sum_probs=28.9
Q ss_pred CCCCeE-EEEEEEEcCCCCCCeeEEEEEEEEcC
Q 032005 95 IAAGDF-VLSHTQTLPSFTPPGSYTLKMTMEDK 126 (149)
Q Consensus 95 l~~G~~-~~~~~~~ip~~~P~g~~~v~~~l~d~ 126 (149)
++||++ +-+.++.+|+..++|.|.++++.+.+
T Consensus 438 L~pge~~tV~ltI~vP~~a~aGdY~i~i~~ksD 470 (513)
T COG1470 438 LEPGESKTVSLTITVPEDAGAGDYRITITAKSD 470 (513)
T ss_pred cCCCCcceEEEEEEcCCCCCCCcEEEEEEEeec
Confidence 789994 88999999999999999999999865
No 52
>PF15432 Sec-ASP3: Accessory Sec secretory system ASP3
Probab=74.57 E-value=11 Score=26.03 Aligned_cols=37 Identities=30% Similarity=0.515 Sum_probs=26.6
Q ss_pred CCCC-CCCe-EEEEEEEEcCCCCCCeeEEEEEEEEcCCCCEE
Q 032005 92 SCPI-AAGD-FVLSHTQTLPSFTPPGSYTLKMTMEDKNNEEL 131 (149)
Q Consensus 92 ~CPl-~~G~-~~~~~~~~ip~~~P~g~~~v~~~l~d~~~~~~ 131 (149)
.=|+ ++|+ |.+...+.. .|.+.+.+++.++|..|+.+
T Consensus 46 ~LPlLk~G~~Y~l~~~~~~---~P~~svylki~F~dr~~e~i 84 (128)
T PF15432_consen 46 SLPLLKRGHTYQLKFNIDV---VPENSVYLKIIFFDRQGEEI 84 (128)
T ss_pred CCCEecCCCEEEEEEEEEE---ccCCeEEEEEEEEccCCCEe
Confidence 3444 5665 666666654 37889999999999988765
No 53
>PLN02792 oxidoreductase
Probab=74.56 E-value=6.3 Score=33.81 Aligned_cols=54 Identities=17% Similarity=0.351 Sum_probs=28.8
Q ss_pred CCCCCcEEEEEEEEeCeEecccEEEEEEEECCEEeccC-CcCCCCCCCCCCCCCe-EEEEEEE
Q 032005 46 VVTGKPATFNISAVTGQAVYGGKVVINVAYFGVPVHQE-TRDVCEEVSCPIAAGD-FVLSHTQ 106 (149)
Q Consensus 46 ~~~G~~~~i~~~~~~~~~i~~~~~~v~~~~~gi~v~~~-~~d~C~~~~CPl~~G~-~~~~~~~ 106 (149)
.++|+++.|++.=.+++. ..+.+-|+..+.. ..|.=.++.||++||+ |+|+++.
T Consensus 51 ~~~GD~v~V~v~N~L~~~-------ttiHWHGl~q~~~~~~DGv~~tqcPI~PG~sftY~F~~ 106 (536)
T PLN02792 51 SLTNDNLVINVHNDLDEP-------FLLSWNGVHMRKNSYQDGVYGTTCPIPPGKNYTYDFQV 106 (536)
T ss_pred EECCCEEEEEEEeCCCCC-------cCEeCCCcccCCCCccCCCCCCcCccCCCCcEEEEEEe
Confidence 355555555554333211 1234556555432 2333234789999998 7776664
No 54
>PF13754 Big_3_4: Bacterial Ig-like domain (group 3)
Probab=74.12 E-value=11 Score=21.76 Aligned_cols=34 Identities=32% Similarity=0.551 Sum_probs=23.3
Q ss_pred EcCCCCCCeeEEEEEEEEcCCCCEEEEEEEEEEEc
Q 032005 107 TLPSFTPPGSYTLKMTMEDKNNEELTCFSFNFKIG 141 (149)
Q Consensus 107 ~ip~~~P~g~~~v~~~l~d~~~~~~~C~~~~v~i~ 141 (149)
.+|.. ..|.|.++++..|.-|..-.-....|.|.
T Consensus 17 t~~~~-~dG~y~itv~a~D~AGN~s~~~~~~~tiD 50 (54)
T PF13754_consen 17 TVPAL-ADGTYTITVTATDAAGNTSTSSSVTFTID 50 (54)
T ss_pred eCCCC-CCccEEEEEEEEeCCCCCCCccceeEEEe
Confidence 44544 68999999999998876544444445543
No 55
>PF09551 Spore_II_R: Stage II sporulation protein R (spore_II_R); InterPro: IPR014202 This entry is designated stage II sporulation protein R. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. SpoIIR is a signalling protein that links the activation of sigma E to the transcriptional activity of sigma F during sporulation [, ].
Probab=71.44 E-value=5.3 Score=27.78 Aligned_cols=26 Identities=27% Similarity=0.650 Sum_probs=22.5
Q ss_pred CCCeeE-EEEEEEEcCCCCEEEEEEEE
Q 032005 112 TPPGSY-TLKMTMEDKNNEELTCFSFN 137 (149)
Q Consensus 112 ~P~g~~-~v~~~l~d~~~~~~~C~~~~ 137 (149)
+|.|.| .+++.+=+..|++-.|+.||
T Consensus 93 ~PaG~YeAlrI~IG~g~G~NWWCVLfP 119 (130)
T PF09551_consen 93 LPAGEYEALRITIGEGKGHNWWCVLFP 119 (130)
T ss_pred ccCCceEEEEEEecCccCcceEEEecC
Confidence 799999 56888877889999999987
No 56
>PF07732 Cu-oxidase_3: Multicopper oxidase; InterPro: IPR011707 Copper is one of the most prevalent transition metals in living organisms and its biological function is intimately related to its redox properties. Since free copper is toxic, even at very low concentrations, its homeostasis in living organisms is tightly controlled by subtle molecular mechanisms. In eukaryotes, before being transported inside the cell via the high-affinity copper transporters of the CTR family, the copper (II) ion is reduced to copper (I). In blue copper proteins such as cupredoxin, the copper (I) ion form is stabilised by a constrained His2Cys coordination environment. Multicopper oxidases oxidise their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre; dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water []. There are three spectroscopically different copper centres found in multicopper oxidases: type 1 (or blue), type 2 (or normal) and type 3 (or coupled binuclear) [, ]. Multicopper oxidases consist of 2, 3 or 6 of these homologous domains, which also share homology to the cupredoxins azurin and plastocyanin. Structurally, these domains consist of a cupredoxin-like fold, a beta-sandwich consisting of 7 strands in 2 beta-sheets, arranged in a Greek-key beta-barrel []. Multicopper oxidases include: Ceruloplasmin (1.16.3.1 from EC) (ferroxidase), a 6-domain enzyme found in the serum of mammals and birds that oxidizes different inorganic and organic substances; exhibits internal sequence homology that appears to have evolved from the triplication of a Cu-binding domain similar to that of laccase and ascorbate oxidase. Laccase (1.10.3.2 from EC) (urishiol oxidase), a 3-domain enzyme found in fungi and plants, which oxidizes different phenols and diamines. CueO is a laccase found in Escherichia coli that is involved in copper-resistance []. Ascorbate oxidase (1.10.3.3 from EC), a 3-domain enzyme found in higher plants. Nitrite reductase (1.7.2.1 from EC), a 2-domain enzyme containing type-1 and type-2 copper centres [, ]. In addition to the above enzymes there are a number of other proteins that are similar to the multi-copper oxidases in terms of structure and sequence, some of which have lost the ability to bind copper. These include: copper resistance protein A (copA) from a plasmid in Pseudomonas syringae; domain A of (non-copper binding) blood coagulation factors V (Fa V) and VIII (Fa VIII) []; yeast FET3 required for ferrous iron uptake []; yeast hypothetical protein YFL041w; and the fission yeast homologue SpAC1F7.08. This entry represents multicopper oxidase type 3 (or coupled binuclear) domains. ; GO: 0005507 copper ion binding; PDB: 2QT6_B 3KW7_B 2R7E_A 3CDZ_A 1SDD_A 3G5W_D 3UAC_A 2YXV_A 3OD3_A 3NSY_A ....
Probab=71.32 E-value=4.6 Score=27.26 Aligned_cols=61 Identities=23% Similarity=0.443 Sum_probs=30.5
Q ss_pred CCCCCcEEEEEEEEeCeEecccEEEEEEEECCEEeccC-CcC-CCCCCCCCCCCCe-EEEEEEEEcCCCCCCeeE
Q 032005 46 VVTGKPATFNISAVTGQAVYGGKVVINVAYFGVPVHQE-TRD-VCEEVSCPIAAGD-FVLSHTQTLPSFTPPGSY 117 (149)
Q Consensus 46 ~~~G~~~~i~~~~~~~~~i~~~~~~v~~~~~gi~v~~~-~~d-~C~~~~CPl~~G~-~~~~~~~~ip~~~P~g~~ 117 (149)
+++|+++.|++.=.+.... .+.+-|+..+.. ..| .-....||+.||+ ++|.+ .++. ++|.|
T Consensus 30 v~~Gd~v~i~~~N~l~~~~-------siH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~Y~~--~~~~--~~Gt~ 93 (117)
T PF07732_consen 30 VREGDTVRITVTNNLDEPT-------SIHWHGLHQPPSPWMDGVPGVTQCPIAPGESFTYEF--TANQ--QAGTY 93 (117)
T ss_dssp EETTEEEEEEEEEESSSGB-------SEEEETSBSTTGGGGSGGTTTSGSSBSTTEEEEEEE--EESS--CSEEE
T ss_pred EEcCCeeEEEEEecccccc-------ccccceeeeeeeeecCCcccccceeEEeecceeeeE--eeec--cccce
Confidence 3566666666654443321 123334433322 122 2223679999998 55544 4443 45654
No 57
>PF06775 Seipin: Putative adipose-regulatory protein (Seipin); InterPro: IPR009617 Seipin is a protein of approximately 400 residues in humans, which is the product of a gene homologous to the murine guanine nucleotide-binding protein (G protein) gamma-3 linked gene. This gene is implicated in the regulation of body fat distribution and insulin resistance and particularly in the auto-immune disease Berardinelli-Seip congenital lipodystrophy type 2. Seipin has no similarity with other known proteins or consensus motifs that might predict its function, but it is predicted to contain two transmembrane domains at residues 28-49 and 237-258, in humans, and a third transmembrane domain might be present at residues 155-173. Seipin may also be implicated in Silver spastic paraplegia syndrome and distal hereditary motor neuropathy type V [].
Probab=70.96 E-value=19 Score=26.62 Aligned_cols=44 Identities=18% Similarity=0.265 Sum_probs=33.7
Q ss_pred CCCCe-EEEEEEEEcCCC---CCCeeEEEEEEEEcCCCCEEEEEEEEE
Q 032005 95 IAAGD-FVLSHTQTLPSF---TPPGSYTLKMTMEDKNNEELTCFSFNF 138 (149)
Q Consensus 95 l~~G~-~~~~~~~~ip~~---~P~g~~~v~~~l~d~~~~~~~C~~~~v 138 (149)
+.+|+ |..+..+.+|.. .--|.+.+.+++.+++|+.+.=..=+.
T Consensus 53 l~~~q~Ydv~v~L~lP~S~~N~~lG~Fmv~l~l~s~~~~~l~~s~Rp~ 100 (199)
T PF06775_consen 53 LPPGQPYDVSVELELPESPYNRDLGMFMVSLELLSANGKVLASSSRPA 100 (199)
T ss_pred cCCCceEEEEEEEEeCCCCCcCCCCeEEEEEEEEcCCCcEEEEEecce
Confidence 66788 888888889865 455899999999999998765433333
No 58
>PF03067 Chitin_bind_3: Chitin binding domain; InterPro: IPR004302 Entomopoxviruses are a class of insect viruses whose virions are embedded in cytoplasmic occlusion bodies. The major component of these protective complexes is a protein called spheroidin/spindolin. Intermolecular disulphide bonds have been shown to play major roles in the formation and structure of these viral occlusion bodies [] some of which are spindle body proteins.; GO: 0019028 viral capsid; PDB: 3UAM_E 2XWX_A 2LHS_A 2BEM_B 2BEN_B 4A02_A.
Probab=68.67 E-value=32 Score=24.80 Aligned_cols=88 Identities=15% Similarity=0.120 Sum_probs=41.8
Q ss_pred CCCCcEEEEEEEEeCeEecccEEEEEEEECCEEe--c-cCCcCCCCCCCCCC--------CCCeEEEEEEEEcCCCCCCe
Q 032005 47 VTGKPATFNISAVTGQAVYGGKVVINVAYFGVPV--H-QETRDVCEEVSCPI--------AAGDFVLSHTQTLPSFTPPG 115 (149)
Q Consensus 47 ~~G~~~~i~~~~~~~~~i~~~~~~v~~~~~gi~v--~-~~~~d~C~~~~CPl--------~~G~~~~~~~~~ip~~~P~g 115 (149)
+.|+++.|++.+++++ ..+..++.+.-.+... + ....++-....|.+ .++...|++++.||.. ..|
T Consensus 82 ~~G~~i~~~~~~ta~H--~~g~~~~~itk~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~v~lP~~-~~g 158 (183)
T PF03067_consen 82 TPGQTIDFKWNITAPH--GTGYFEFYITKPGWDPTEPCLTWDDLELIPFCQYDNPGQDPGPADQTNYTMSVTLPDG-RCG 158 (183)
T ss_dssp ESE-EEEEEEEESS-S---EEEEEEEEB-TT--TTS----GGGBESSESEEEEEEEEHHHSSSEEEE--EEEE-TT---E
T ss_pred CCCCeEEEEEEEeccc--CCeeEEEEEcCCCCCcCccccchhhccccCceeecCCCcCcCCCCCceEEEEEECCCC-CcC
Confidence 6788888888888877 3445555554333321 0 00111111111221 1444677889999987 678
Q ss_pred eEEEEEEEEcCCCC--E-EEEEEEE
Q 032005 116 SYTLKMTMEDKNNE--E-LTCFSFN 137 (149)
Q Consensus 116 ~~~v~~~l~d~~~~--~-~~C~~~~ 137 (149)
+..++|.=...+.. . ..|+.+.
T Consensus 159 ~~Vl~~~W~~~~~~~E~F~~C~Dv~ 183 (183)
T PF03067_consen 159 HCVLQWRWQRGDSWGETFYNCSDVT 183 (183)
T ss_dssp EEEEEEEEEETTSSE-EEEEEEEEE
T ss_pred CEEEEEEEEeccCCCCeEEeeEccC
Confidence 77776655544433 3 5788763
No 59
>KOG3780 consensus Thioredoxin binding protein TBP-2/VDUP1 [General function prediction only]
Probab=67.72 E-value=9.4 Score=31.16 Aligned_cols=31 Identities=26% Similarity=0.545 Sum_probs=25.8
Q ss_pred CCCCeEEEEEEEEcCCCCCC--------eeEEEEEEEEc
Q 032005 95 IAAGDFVLSHTQTLPSFTPP--------GSYTLKMTMED 125 (149)
Q Consensus 95 l~~G~~~~~~~~~ip~~~P~--------g~~~v~~~l~d 125 (149)
+.+|.|+|.+.+.||..+|+ ++|.+++++.-
T Consensus 102 l~~G~~~~pF~~~LP~~~P~Sfeg~~G~irY~vk~~idr 140 (427)
T KOG3780|consen 102 LPPGNYEFPFSFTLPLNLPPSFEGKFGHVRYFVKAEIDR 140 (427)
T ss_pred cCCCceEEeEeccCCCCCCCceeeCCceEEEEEEEEEec
Confidence 88999999999999977766 57888888853
No 60
>TIGR01480 copper_res_A copper-resistance protein, CopA family. This model represents the CopA copper resistance protein family. CopA is related to laccase (benzenediol:oxygen oxidoreductase) and L-ascorbate oxidase, both copper-containing enzymes. Most members have a typical TAT (twin-arginine translocation) signal sequence with an Arg-Arg pair. Twin-arginine translocation is observed for a large number of periplasmic proteins that cross the inner membrane with metal-containing cofactors already bound. The combination of copper-binding sites and TAT translocation motif suggests a mechansism of resistance by packaging and export.
Probab=66.22 E-value=12 Score=32.51 Aligned_cols=16 Identities=25% Similarity=0.343 Sum_probs=12.5
Q ss_pred CCCCCCCCe-EEEEEEE
Q 032005 91 VSCPIAAGD-FVLSHTQ 106 (149)
Q Consensus 91 ~~CPl~~G~-~~~~~~~ 106 (149)
..||+.||+ ++|.++.
T Consensus 118 t~~~I~PG~s~~Y~f~~ 134 (587)
T TIGR01480 118 SFAGIAPGETFTYRFPV 134 (587)
T ss_pred cccccCCCCeEEEEEEC
Confidence 469999998 6776664
No 61
>TIGR02837 spore_II_R stage II sporulation protein R. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is designated stage II sporulation protein R.
Probab=63.80 E-value=8.8 Score=27.85 Aligned_cols=26 Identities=23% Similarity=0.597 Sum_probs=22.5
Q ss_pred CCCeeE-EEEEEEEcCCCCEEEEEEEE
Q 032005 112 TPPGSY-TLKMTMEDKNNEELTCFSFN 137 (149)
Q Consensus 112 ~P~g~~-~v~~~l~d~~~~~~~C~~~~ 137 (149)
+|.|.| .+++.+=+.+|++-.|+.||
T Consensus 128 ~PaG~YeAlrI~IG~g~G~NWWCVlfP 154 (168)
T TIGR02837 128 LPAGEYEALRILIGEGAGANWWCVVFP 154 (168)
T ss_pred ccCCceEEEEEEecCcCCcceEEEecC
Confidence 799999 46888878889999999987
No 62
>PF15240 Pro-rich: Proline-rich
Probab=63.54 E-value=4.5 Score=29.66 Aligned_cols=15 Identities=47% Similarity=0.594 Sum_probs=8.3
Q ss_pred ehHHHHHHHhhhccC
Q 032005 5 LMLFACFLLLVSSTQ 19 (149)
Q Consensus 5 ~~l~~~~~~~~~~~~ 19 (149)
||||.++|||+++|+
T Consensus 3 lVLLSvALLALSSAQ 17 (179)
T PF15240_consen 3 LVLLSVALLALSSAQ 17 (179)
T ss_pred hHHHHHHHHHhhhcc
Confidence 344445566666655
No 63
>cd00917 PG-PI_TP The phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP) has been shown to bind phosphatidylglycerol and phosphatidylinositol, but the biological significance of this is still obscure. These proteins belong to the ML domain family.
Probab=62.70 E-value=25 Score=23.71 Aligned_cols=32 Identities=16% Similarity=0.252 Sum_probs=24.1
Q ss_pred CCCCCCCCe-EEEEEEEEcCCCCCCe-eEEEEEE
Q 032005 91 VSCPIAAGD-FVLSHTQTLPSFTPPG-SYTLKMT 122 (149)
Q Consensus 91 ~~CPl~~G~-~~~~~~~~ip~~~P~g-~~~v~~~ 122 (149)
.+||+.+|+ .+++.++.....+..| +..+.++
T Consensus 20 sP~p~~~G~~~ti~~~~~~~~~v~~g~~~~v~~~ 53 (122)
T cd00917 20 SPNPPAAGQNLTIEASGSVGKEIEDGAYVVVEVK 53 (122)
T ss_pred ECCCcCCCCcEEEEEEEEECcCcCCCCEEEEEEE
Confidence 478999998 8888888888777776 5554443
No 64
>PRK12633 flgD flagellar basal body rod modification protein; Provisional
Probab=61.06 E-value=15 Score=27.97 Aligned_cols=37 Identities=14% Similarity=0.253 Sum_probs=22.7
Q ss_pred CCCCeEEEEEEE--EcCCCCCCeeEEEEEEEEcCCCCEE
Q 032005 95 IAAGDFVLSHTQ--TLPSFTPPGSYTLKMTMEDKNNEEL 131 (149)
Q Consensus 95 l~~G~~~~~~~~--~ip~~~P~g~~~v~~~l~d~~~~~~ 131 (149)
..+|.+.|...- .=-..+|.|.|++++...+.+|+.+
T Consensus 151 ~~aG~~~f~WDG~d~~G~~~~~G~Y~~~V~a~~~~G~~~ 189 (230)
T PRK12633 151 LKTGVHTLQWDGNNDGGQPLADGKYSITVSASDADAKPV 189 (230)
T ss_pred CCCCceeEEECCCCCCCCcCCCcceEEEEEEEeCCCcEE
Confidence 456764443332 2223468888888888887777654
No 65
>PRK12634 flgD flagellar basal body rod modification protein; Reviewed
Probab=60.79 E-value=16 Score=27.63 Aligned_cols=36 Identities=22% Similarity=0.285 Sum_probs=20.2
Q ss_pred CCCCeEEEEEEEE--cCCCCCCeeEEEEEEEEcCCCCE
Q 032005 95 IAAGDFVLSHTQT--LPSFTPPGSYTLKMTMEDKNNEE 130 (149)
Q Consensus 95 l~~G~~~~~~~~~--ip~~~P~g~~~v~~~l~d~~~~~ 130 (149)
..+|.+.|...-. =-...|.|.|++++.-.+.+|+.
T Consensus 144 ~~aG~~~f~WDG~d~~G~~~~~G~Yt~~v~a~~~~G~~ 181 (221)
T PRK12634 144 SAAGEVSFAWDGTDANGNRMAAGKYGVTATQTDTAGSK 181 (221)
T ss_pred cCCCceeEEECCCCCCCCcCCCeeeEEEEEEEeCCCcE
Confidence 4567644333322 12336777787777777666653
No 66
>KOG4063 consensus Major epididymal secretory protein HE1 [Function unknown]
Probab=60.72 E-value=20 Score=25.59 Aligned_cols=33 Identities=18% Similarity=0.095 Sum_probs=26.5
Q ss_pred CCCCCCCcEEEEEEEEeCeEecccEEEEEEEEC
Q 032005 44 DPVVTGKPATFNISAVTGQAVYGGKVVINVAYF 76 (149)
Q Consensus 44 c~~~~G~~~~i~~~~~~~~~i~~~~~~v~~~~~ 76 (149)
||+.+|++++....+-...+..+..+.+.+.+.
T Consensus 108 CPl~age~ytY~~slpI~~~yP~v~v~iew~L~ 140 (158)
T KOG4063|consen 108 CPLSAGEDYTYLNSLPITENYPEVSVIIEWQLQ 140 (158)
T ss_pred CcccCCCceEEEEEeeccccCCceeEEEEEEEe
Confidence 899999999999998888777777766665554
No 67
>PF11797 DUF3324: Protein of unknown function C-terminal (DUF3324); InterPro: IPR021759 This family consists of several hypothetical bacterial proteins of unknown function.
Probab=60.54 E-value=41 Score=23.34 Aligned_cols=45 Identities=27% Similarity=0.375 Sum_probs=29.7
Q ss_pred CCCCeEEEEEEEEcC-CCCCCeeEEEEEEEEcCCCCEEEEEEEEEEEcc
Q 032005 95 IAAGDFVLSHTQTLP-SFTPPGSYTLKMTMEDKNNEELTCFSFNFKIGF 142 (149)
Q Consensus 95 l~~G~~~~~~~~~ip-~~~P~g~~~v~~~l~d~~~~~~~C~~~~v~i~~ 142 (149)
++|.. .|.+.+.+. ..+++|+|+++++++.+++ -.=|+=+|+|..
T Consensus 86 mAPNS-~f~~~i~~~~~~lk~G~Y~l~~~~~~~~~--~W~f~k~F~It~ 131 (140)
T PF11797_consen 86 MAPNS-NFNFPIPLGGKKLKPGKYTLKITAKSGKK--TWTFTKDFTITA 131 (140)
T ss_pred ECCCC-eEEeEecCCCcCccCCEEEEEEEEEcCCc--EEEEEEEEEECH
Confidence 44443 334444443 6789999999999997655 345666777655
No 68
>PF12690 BsuPI: Intracellular proteinase inhibitor; InterPro: IPR020481 BsuPI is a intracellular proteinase inhibitor that directly regulates the major intracellular proteinase (ISP-1) activity in vivo. It inhibits ISP-1 in the early stages of sporulation and then may be inactivated by a membrane-bound proteinase [].; PDB: 3ISY_A.
Probab=59.43 E-value=13 Score=23.49 Aligned_cols=26 Identities=31% Similarity=0.659 Sum_probs=16.0
Q ss_pred CCCCe-EEEEEEEEcCCCCCCeeEEEEE
Q 032005 95 IAAGD-FVLSHTQTLPSFTPPGSYTLKM 121 (149)
Q Consensus 95 l~~G~-~~~~~~~~ip~~~P~g~~~v~~ 121 (149)
++||+ .+|..++..++.- +|.|++++
T Consensus 56 l~pGe~~~~~~~~~~~~~~-~G~Y~~~a 82 (82)
T PF12690_consen 56 LEPGESLTYEETWDLKDLS-PGEYTLEA 82 (82)
T ss_dssp E-TT-EEEEEEEESS-----SEEEEEEE
T ss_pred ECCCCEEEEEEEECCCCCC-CceEEEeC
Confidence 78998 6888777766544 79999874
No 69
>PF02494 HYR: HYR domain; InterPro: IPR003410 This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion. In the Sushi repeat-containing protein (SrpX), this domain is found between two sushi repeats.
Probab=59.10 E-value=16 Score=22.60 Aligned_cols=25 Identities=28% Similarity=0.450 Sum_probs=20.7
Q ss_pred CCCCCeeEEEEEEEEcCCCCEEEEE
Q 032005 110 SFTPPGSYTLKMTMEDKNNEELTCF 134 (149)
Q Consensus 110 ~~~P~g~~~v~~~l~d~~~~~~~C~ 134 (149)
..+|.|.+.|+++.+|..|..-.|.
T Consensus 52 ~~f~~G~t~V~ytA~D~~GN~a~C~ 76 (81)
T PF02494_consen 52 DLFPVGTTTVTYTATDAAGNSATCS 76 (81)
T ss_pred ceEeeceEEEEEEEEECCCCEEEEE
Confidence 4577899999999999988776773
No 70
>TIGR03711 acc_sec_asp3 accessory Sec system protein Asp3. This protein is designated Asp3 because, along with SecY2, SecA2, and other proteins it is part of the accessory Sec system. The system is involved in the export of serine-rich glycoproteins important for virulence in a number of Gram-positive species, including Streptococcus gordonii and Staphylococcus aureus. This protein family is assigned to transport rather than glycosylation function, but the specific molecular role is unknown.
Probab=58.68 E-value=23 Score=24.83 Aligned_cols=40 Identities=28% Similarity=0.346 Sum_probs=27.3
Q ss_pred CCCCCCCCeEEEEEEEEcCCCCCCeeEEEEEEEEcCCCCEE
Q 032005 91 VSCPIAAGDFVLSHTQTLPSFTPPGSYTLKMTMEDKNNEEL 131 (149)
Q Consensus 91 ~~CPl~~G~~~~~~~~~ip~~~P~g~~~v~~~l~d~~~~~~ 131 (149)
+.=|+-++..+|...+.+- ..|.+.+.+++.+.|..++++
T Consensus 56 P~LPlLk~g~~Y~i~~n~~-~~P~~s~~~ki~F~dr~~~ei 95 (135)
T TIGR03711 56 PSLPLLKRGQTYKLSLNAD-ASPEGSVYLKITFFDRQGEEI 95 (135)
T ss_pred CCCcEEcCCCEEEEEEeee-eCCCceEEEEEEEeccCCcee
Confidence 4556655554444444432 467899999999999988765
No 71
>PRK10350 hypothetical protein; Provisional
Probab=58.25 E-value=4.6 Score=27.94 Aligned_cols=26 Identities=31% Similarity=0.356 Sum_probs=18.9
Q ss_pred CcceehHHHHHHHhhhccCccceeeCC
Q 032005 1 MDRQLMLFACFLLLVSSTQAIGVKYCD 27 (149)
Q Consensus 1 m~~~~~l~~~~~~~~~~~~~~~~~~C~ 27 (149)
|.|++ +|++||.++++|+.++--+=.
T Consensus 1 MKr~L-~~~allP~~~~AqplN~~NNP 26 (145)
T PRK10350 1 MKRLL-LLTALLPFVGFAQPINTLNNP 26 (145)
T ss_pred ChhHH-HHHHHhHHHHHHhhhhccCCC
Confidence 77875 667788888888877655443
No 72
>PF13750 Big_3_3: Bacterial Ig-like domain (group 3)
Probab=55.53 E-value=59 Score=23.14 Aligned_cols=47 Identities=26% Similarity=0.389 Sum_probs=30.0
Q ss_pred CCCeEEEEEEEEcCCCCCCeeEEEEEEEEcCCCCEEEEEEEEEEEccc
Q 032005 96 AAGDFVLSHTQTLPSFTPPGSYTLKMTMEDKNNEELTCFSFNFKIGFH 143 (149)
Q Consensus 96 ~~G~~~~~~~~~ip~~~P~g~~~v~~~l~d~~~~~~~C~~~~v~i~~~ 143 (149)
..|.|.+.+...+|+.-+.+.|++++...|..|.+ .=-.+.|.....
T Consensus 104 ~~~~~~~~yp~~fpsle~~~~YtLtV~a~D~aGN~-~~~si~F~y~P~ 150 (158)
T PF13750_consen 104 GNGVYTLEYPRIFPSLEADDSYTLTVSATDKAGNQ-STKSISFSYMPP 150 (158)
T ss_pred cCceEEeecccccCCcCCCCeEEEEEEEEecCCCE-EEEEEEEEEeCC
Confidence 34556666655566666678999999999988754 233344444443
No 73
>TIGR03389 laccase laccase, plant. Members of this protein family include the copper-containing enzyme laccase (EC 1.10.3.2), often several from a single plant species, and additional, uncharacterized, closely related plant proteins termed laccase-like multicopper oxidases. This protein family shows considerable sequence similarity to the L-ascorbate oxidase (EC 1.10.3.3) family. Laccases are enzymes of rather broad specificity, and classification of all proteins scoring about the trusted cutoff of this model as laccases may be appropriate.
Probab=53.07 E-value=52 Score=28.17 Aligned_cols=16 Identities=38% Similarity=0.850 Sum_probs=12.6
Q ss_pred CCCCCCCCe-EEEEEEE
Q 032005 91 VSCPIAAGD-FVLSHTQ 106 (149)
Q Consensus 91 ~~CPl~~G~-~~~~~~~ 106 (149)
+.||+.||+ ++|.+..
T Consensus 78 Tq~pI~PG~s~~Y~f~~ 94 (539)
T TIGR03389 78 TQCPIQPGQSYVYNFTI 94 (539)
T ss_pred ccCCcCCCCeEEEEEEe
Confidence 589999998 6666654
No 74
>PF04729 ASF1_hist_chap: ASF1 like histone chaperone; InterPro: IPR006818 This family includes the yeast and human ASF1 protein. These proteins have histone chaperone activity []. ASF1 participates in both the replication-dependent and replication-independent pathways. The structure three-dimensional has been determined as a compact immunoglobulin-like beta sandwich fold topped by three helical linkers [].; GO: 0006333 chromatin assembly or disassembly, 0005634 nucleus; PDB: 2YGV_C 1WG3_A 2HUE_A 2IDC_A 4EO5_A 1ROC_A 1TEY_A 2IO5_A 3AAD_D 2IIJ_A ....
Probab=52.80 E-value=38 Score=24.28 Aligned_cols=77 Identities=19% Similarity=0.336 Sum_probs=46.7
Q ss_pred cEEEeEEEEeCCCCCCCCcEEEEEEEEeCeEecccEEEEEEEECCEEeccCCcCCCC-----CCCCCCCCCeEEEEEEEE
Q 032005 33 AVTIQQVKIIPDPVVTGKPATFNISAVTGQAVYGGKVVINVAYFGVPVHQETRDVCE-----EVSCPIAAGDFVLSHTQT 107 (149)
Q Consensus 33 ~~~i~~~~i~Pc~~~~G~~~~i~~~~~~~~~i~~~~~~v~~~~~gi~v~~~~~d~C~-----~~~CPl~~G~~~~~~~~~ 107 (149)
.++|+++++...|-.-..+..++++|...+++++. +++++.|-|. ...+--+ -.-=|+..|.+.|.+...
T Consensus 3 ~V~l~~V~vl~np~~f~~p~~feI~fE~~e~L~~d-leWkiiYVgS----a~~~~~DQ~Ld~v~vGPi~~G~~kF~~~ad 77 (154)
T PF04729_consen 3 RVNLTNVEVLNNPAPFTDPFQFEITFECLEPLEDD-LEWKIIYVGS----AESEEYDQELDSVLVGPIPVGVNKFVFEAD 77 (154)
T ss_dssp SEEEEEEEESSTSEETTS-EEEEEEEEESSE-SS--EEEEEEEESS----SSSGGGEEEEEEEEECS-ESEEEEEEEEE-
T ss_pred eEEEEEEEEeCCccccCCCEEEEEEEEECccccCC-cEEEEEEEec----ccccCCcEEEeeEEECCCcceeEEEEEEcc
Confidence 57899999998888888999999999999987543 4555544331 1111111 134588899866666655
Q ss_pred cC--CCCCC
Q 032005 108 LP--SFTPP 114 (149)
Q Consensus 108 ip--~~~P~ 114 (149)
-| ..+|.
T Consensus 78 pPd~~~Ip~ 86 (154)
T PF04729_consen 78 PPDPSKIPP 86 (154)
T ss_dssp ---GGGSSC
T ss_pred CCChhhCCh
Confidence 44 44664
No 75
>PRK12812 flgD flagellar basal body rod modification protein; Reviewed
Probab=51.93 E-value=26 Score=27.29 Aligned_cols=21 Identities=33% Similarity=0.694 Sum_probs=13.2
Q ss_pred CCCCeeEEEEEEEEcCCCCEE
Q 032005 111 FTPPGSYTLKMTMEDKNNEEL 131 (149)
Q Consensus 111 ~~P~g~~~v~~~l~d~~~~~~ 131 (149)
.+|.|.|++++...+.+|+.+
T Consensus 181 ~~~~G~Yt~~v~A~~~~G~~~ 201 (259)
T PRK12812 181 YAGDGEYTIKAVYNNKNGEKI 201 (259)
T ss_pred cCCCeeeEEEEEEEcCCCcEE
Confidence 356677777777666666543
No 76
>PF04379 DUF525: Protein of unknown function (DUF525); InterPro: IPR007474 This domain is found in the bacterial protein ApaG and at the C termini of some F-box proteins (IPR001810 from INTERPRO). F-box proteins contain a carboxy-terminal domain that interacts with protein substrates []. The ApaG domain is ~125 amino acids in length, and is named after the bacterial ApaG protein, of which it forms the core. The Salmonella typhimurium ApaG domain protein, CorD, is involved in Co(2+) resistance and Mg(2+) efflux. Tertiary structures from different ApaG proteins show a fold of several beta-sheets. The ApaG domain may be involved in protein-protein interactions which could be implicated in substrate-specificity [, , ].; PDB: 2F1E_A 1XVS_A 1TZA_A 1XQ4_D.
Probab=50.78 E-value=25 Score=22.72 Aligned_cols=34 Identities=35% Similarity=0.541 Sum_probs=22.3
Q ss_pred CCC-CCCCe-EEEEEEEEcCCCCCCeeEEEEEEEEcCC
Q 032005 92 SCP-IAAGD-FVLSHTQTLPSFTPPGSYTLKMTMEDKN 127 (149)
Q Consensus 92 ~CP-l~~G~-~~~~~~~~ip~~~P~g~~~v~~~l~d~~ 127 (149)
..| |.||+ |+|+....+. .|.|.....+++.++|
T Consensus 55 ~~P~L~pGe~f~Y~S~~~l~--t~~G~M~G~y~~~~~~ 90 (90)
T PF04379_consen 55 QQPVLAPGESFEYTSGCPLS--TPSGSMEGSYTMVDED 90 (90)
T ss_dssp B--EE-TTEEEEEEEEEEES--SSEEEEEEEEEEEET-
T ss_pred cCceECCCCcEEEcCCCCcC--CCCEEEEEEEEEEECc
Confidence 344 47898 6666666665 4779999999988764
No 77
>cd00915 MD-1_MD-2 MD-1 and MD-2 are cofactors required for LPS signaling through cell surface receptors. MD-2 and its binding partner, Toll-like receptor 4 (TLR4), are essential for the innate immune responses of mammalian cells to bacterial lipopolysaccharide (LPS); MD-2 directly binds the lipid A moiety of LPS. The TLR4-like receptor, RP105, which mediates LPS-induced lymphocyte proliferation, interacts with MD-1; MD-1 enhances RP105-mediated LPS-induced growth of B cells. These proteins belong to the ML domain family.
Probab=49.43 E-value=28 Score=24.18 Aligned_cols=33 Identities=9% Similarity=-0.064 Sum_probs=24.1
Q ss_pred eCCCCCCCCcEEEE--EEEEeCeEecccEEEEEEEE
Q 032005 42 IPDPVVTGKPATFN--ISAVTGQAVYGGKVVINVAY 75 (149)
Q Consensus 42 ~Pc~~~~G~~~~i~--~~~~~~~~i~~~~~~v~~~~ 75 (149)
+-||+++|++++-. .++-..+ ...+...+.+.+
T Consensus 81 s~CP~~kGet~~Y~~p~slpi~~-yP~~~y~V~weL 115 (130)
T cd00915 81 SFCGALKGETVYYVGPFSFKGIL-IPQGQYRCVAEL 115 (130)
T ss_pred ccCCccCCceEEEeeeecccccc-cCCccEEEEEEE
Confidence 34999999999999 6666666 666666665554
No 78
>PF11141 DUF2914: Protein of unknown function (DUF2914); InterPro: IPR022606 This bacterial family of proteins has no known function.
Probab=48.37 E-value=59 Score=19.55 Aligned_cols=42 Identities=26% Similarity=0.632 Sum_probs=27.6
Q ss_pred CCCCCeE-EEEEEEEcCCCCCCeeEEEEEEEEcCCCCEEEEEEEEEE
Q 032005 94 PIAAGDF-VLSHTQTLPSFTPPGSYTLKMTMEDKNNEELTCFSFNFK 139 (149)
Q Consensus 94 Pl~~G~~-~~~~~~~ip~~~P~g~~~v~~~l~d~~~~~~~C~~~~v~ 139 (149)
++..|.| +|+.....| -..|+.+|+ +.|++|+.+.=.+|.++
T Consensus 24 ~i~g~r~Rt~S~k~~~~--~~~G~WrV~--V~~~~G~~l~~~~F~Vt 66 (66)
T PF11141_consen 24 PISGGRWRTWSSKQNFP--DQPGDWRVE--VVDEDGQVLGSLRFSVT 66 (66)
T ss_pred eccCCCEEEEEEeecCC--CCCcCEEEE--EEcCCCCEEEEEEEEEC
Confidence 3554446 666666665 456776655 55788999988887763
No 79
>TIGR03390 ascorbOXfungal L-ascorbate oxidase, fungal type. This model describes a family of fungal ascorbate oxidases, within a larger family of multicopper oxidases that also includes plant ascorbate oxidases (TIGR03388), plant laccases and laccase-like proteins (TIGR03389), and related proteins. The member from Acremonium sp. HI-25 is characterized.
Probab=46.28 E-value=41 Score=28.83 Aligned_cols=16 Identities=25% Similarity=0.405 Sum_probs=13.1
Q ss_pred CCCCCCCCe-EEEEEEE
Q 032005 91 VSCPIAAGD-FVLSHTQ 106 (149)
Q Consensus 91 ~~CPl~~G~-~~~~~~~ 106 (149)
+.||+.||+ |+|.++.
T Consensus 84 TQcpI~PG~sf~Y~f~~ 100 (538)
T TIGR03390 84 SQWPIPPGHFFDYEIKP 100 (538)
T ss_pred ccCCCCCCCcEEEEEEe
Confidence 689999998 7777664
No 80
>PF08737 Rgp1: Rgp1; InterPro: IPR014848 Rgp1 forms heterodimer with Ric1 (IPR009771 from INTERPRO) which associates with Golgi membranes and functions as a guanyl-nucleotide exchange factor [].
Probab=44.04 E-value=91 Score=25.87 Aligned_cols=49 Identities=22% Similarity=0.329 Sum_probs=32.3
Q ss_pred CCCCCe-EEEEEEEEcCCCCCC--------eeEEEEEEEEc--CCCCEEEEEEEEEEEcc
Q 032005 94 PIAAGD-FVLSHTQTLPSFTPP--------GSYTLKMTMED--KNNEELTCFSFNFKIGF 142 (149)
Q Consensus 94 Pl~~G~-~~~~~~~~ip~~~P~--------g~~~v~~~l~d--~~~~~~~C~~~~v~i~~ 142 (149)
-++||+ .+|.+++.+|..+|+ ..|.+.+.+.- ..+...-=+.||++|..
T Consensus 114 ~L~pge~k~f~~~~~lP~~lPPsy~g~~i~~~Y~l~vg~~~~~~~~~~~~~~~~Pi~v~~ 173 (415)
T PF08737_consen 114 RLAPGESKSFHFSFTLPKDLPPSYRGKAIKISYSLVVGTQRGSSVNSKVKSIRVPIRVLP 173 (415)
T ss_pred EECCCCcEEEEEEEeCCCCCCCCCcCcEEEEEEEEEEEEEEcCCCCcceEEEEeCEEEee
Confidence 478999 688889999888777 24555544443 12334556778888774
No 81
>PF10029 DUF2271: Predicted periplasmic protein (DUF2271); InterPro: IPR014469 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=43.85 E-value=93 Score=21.68 Aligned_cols=44 Identities=25% Similarity=0.494 Sum_probs=30.3
Q ss_pred CCCCeEEEEEE--EEcCCCCCCeeEEEEEEEEcCCC-CEEEEEEEEEEE
Q 032005 95 IAAGDFVLSHT--QTLPSFTPPGSYTLKMTMEDKNN-EELTCFSFNFKI 140 (149)
Q Consensus 95 l~~G~~~~~~~--~~ip~~~P~g~~~v~~~l~d~~~-~~~~C~~~~v~i 140 (149)
..+|+|.+... ......+|+|.|++.++.--++| ..+ ++++|++
T Consensus 74 ~~~G~~~~~~d~~~~~~~~l~~g~Y~l~vEaarE~g~~~l--~~~~~~l 120 (139)
T PF10029_consen 74 RPPGKYTLSWDGTDDIGNPLPDGGYTLRVEAAREHGGREL--VRIPFPL 120 (139)
T ss_pred CCCCccEEEEEccccccCccCCCcEEEEEEEEEEECCcEE--EEEEEEe
Confidence 56788655554 55667899999999888876654 345 5555555
No 82
>PF13860 FlgD_ig: FlgD Ig-like domain; PDB: 3C12_A 3OSV_A.
Probab=43.42 E-value=21 Score=22.23 Aligned_cols=32 Identities=25% Similarity=0.418 Sum_probs=16.7
Q ss_pred CCCCeEEEEEEEE--cCCCCCCeeEEEEEEEEcC
Q 032005 95 IAAGDFVLSHTQT--LPSFTPPGSYTLKMTMEDK 126 (149)
Q Consensus 95 l~~G~~~~~~~~~--ip~~~P~g~~~v~~~l~d~ 126 (149)
..+|.+.|...-. --...|+|.|+++++..+.
T Consensus 47 ~~~G~~~~~WdG~d~~G~~~~~G~Y~~~v~a~~~ 80 (81)
T PF13860_consen 47 QSAGEHSFTWDGKDDDGNPVPDGTYTFRVTATDG 80 (81)
T ss_dssp CSSEEEEEEE-SB-TTS-B--SEEEEEEEEEEET
T ss_pred cCCceEEEEECCCCCCcCCCCCCCEEEEEEEEeC
Confidence 3556644433322 2245778888888887764
No 83
>PF14734 DUF4469: Domain of unknown function (DUF4469) with IG-like fold
Probab=41.63 E-value=45 Score=22.07 Aligned_cols=23 Identities=26% Similarity=0.343 Sum_probs=18.2
Q ss_pred EEEEEcCCCCCCeeEEEEEEEEc
Q 032005 103 SHTQTLPSFTPPGSYTLKMTMED 125 (149)
Q Consensus 103 ~~~~~ip~~~P~g~~~v~~~l~d 125 (149)
...+.+|..++.|.|+++++=.-
T Consensus 65 ~l~~~lPa~L~~G~Y~l~V~Tq~ 87 (102)
T PF14734_consen 65 RLIFILPADLAAGEYTLEVRTQY 87 (102)
T ss_pred EEEEECcCccCceEEEEEEEEEe
Confidence 55667899999999998877553
No 84
>cd03451 FkbR2 FkbR2 is a Streptomyces hygroscopicus protein with a hot dog fold that belongs to a conserved family of proteins found in prokaryotes and archaea but not in eukaryotes. FkbR2 has sequence similarity to (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. The function of FkbR2 is unknown.
Probab=40.55 E-value=1.1e+02 Score=20.56 Aligned_cols=45 Identities=18% Similarity=0.228 Sum_probs=25.0
Q ss_pred CCCCCCe-EEEEEEEE--cCC--CCCCeeEEEEEEEEcCCCCEEEEEEEE
Q 032005 93 CPIAAGD-FVLSHTQT--LPS--FTPPGSYTLKMTMEDKNNEELTCFSFN 137 (149)
Q Consensus 93 CPl~~G~-~~~~~~~~--ip~--~~P~g~~~v~~~l~d~~~~~~~C~~~~ 137 (149)
=|+.+|+ .+....+. -+. .-..+-..++.+.+|++|+.++=.+..
T Consensus 90 ~pv~~GDtl~~~~~v~~~~~~~~~~~~~~v~~~~~~~nq~g~~V~~~~~~ 139 (146)
T cd03451 90 APVFHGDTLYAESEVLSKRESKSRPDAGIVTVRTVGYNQDGEPVLSFERT 139 (146)
T ss_pred CCCCCCCEEEEEEEEEEEecCCCCCCCeEEEEEEEEECCCCCEEEEEEeh
Confidence 4788887 44444433 221 112245677888888888765433333
No 85
>TIGR03660 T1SS_rpt_143 T1SS-143 repeat domain. This model represents a domain of about 143 amino acids that may occur singly or in up to 23 tandem repeats in very large proteins in the genus Vibrio, and in related species such as Legionella pneumophila, Photobacterium profundum, Rhodopseudomonas palustris, Shewanella pealeana, and Aeromonas hydrophila. Proteins with these domains represent a subset of a broader set of proteins with a particular signal for type 1 secretion, consisting of several glycine-rich repeats modeled by pfam00353, followed by a C-terminal domain modeled by TIGR03661. Proteins with this domain tend to share several properties with the RtxA (Repeats in Toxin) protein of Vibrio cholerae, including a large size often containing tandemly repeated domains and a C-terminal signal for type 1 secretion.
Probab=39.21 E-value=1.3e+02 Score=20.95 Aligned_cols=48 Identities=8% Similarity=0.101 Sum_probs=29.9
Q ss_pred CeEEEEEEEEcCCCC--CCeeEEEEEEEEcCCCCEEEEEEEEEEEcccccc
Q 032005 98 GDFVLSHTQTLPSFT--PPGSYTLKMTMEDKNNEELTCFSFNFKIGFHSLV 146 (149)
Q Consensus 98 G~~~~~~~~~ip~~~--P~g~~~v~~~l~d~~~~~~~C~~~~v~i~~~~~~ 146 (149)
|.|+|+..-++--.- -.....+.+...|.+|+... ..+.++|.++.|+
T Consensus 66 GsYtftL~~~lDH~~g~d~l~l~~~v~a~D~DGD~s~-~~l~VtI~DD~P~ 115 (137)
T TIGR03660 66 GSYEFTLEGPLDHAAGSDELTLNFPIIATDFDGDTSS-ITLPVTIVDDVPT 115 (137)
T ss_pred ccEEEEEcccccCCCCCceEEEeeeEEEEeCCCCccc-cEEEEEEECCCCe
Confidence 567776666663211 11245556677787776543 4889999887765
No 86
>cd00146 PKD polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases.
Probab=38.44 E-value=82 Score=18.90 Aligned_cols=18 Identities=28% Similarity=0.639 Sum_probs=14.6
Q ss_pred CCeeEEEEEEEEcCCCCE
Q 032005 113 PPGSYTLKMTMEDKNNEE 130 (149)
Q Consensus 113 P~g~~~v~~~l~d~~~~~ 130 (149)
-+|.|+++++..|++|..
T Consensus 55 ~~G~y~v~l~v~d~~g~~ 72 (81)
T cd00146 55 KPGTYTVTLTVTNAVGSS 72 (81)
T ss_pred CCcEEEEEEEEEeCCCCE
Confidence 369999999999987643
No 87
>PF07610 DUF1573: Protein of unknown function (DUF1573); InterPro: IPR011467 These hypothetical proteins from bacteria, such as Rhodopirellula baltica, Bacteroides thetaiotaomicron and Porphyromonas gingivalis, share a region of conserved sequence towards their N termini.
Probab=38.00 E-value=71 Score=17.46 Aligned_cols=34 Identities=12% Similarity=0.264 Sum_probs=20.6
Q ss_pred ceeeCCCCCCccEEEeEEEEe-CC--------CCCCCCcEEEEEEE
Q 032005 22 GVKYCDKKKNYAVTIQQVKII-PD--------PVVTGKPATFNISA 58 (149)
Q Consensus 22 ~~~~C~~~~~~~~~i~~~~i~-Pc--------~~~~G~~~~i~~~~ 58 (149)
.+++-|+. .+.|.++..+ .| ++..|+...|++.|
T Consensus 3 ~~~N~g~~---~L~I~~v~tsCgCt~~~~~~~~i~PGes~~i~v~y 45 (45)
T PF07610_consen 3 EFTNTGDS---PLVITDVQTSCGCTTAEYSKKPIAPGESGKIKVTY 45 (45)
T ss_pred EEEECCCC---cEEEEEeeEccCCEEeeCCcceECCCCEEEEEEEC
Confidence 44555543 6677776543 12 47888888887764
No 88
>PF11614 FixG_C: IG-like fold at C-terminal of FixG, putative oxidoreductase; PDB: 2R39_A.
Probab=36.71 E-value=1.2e+02 Score=19.90 Aligned_cols=37 Identities=22% Similarity=0.331 Sum_probs=23.4
Q ss_pred CCCCe-EEEEEEEEcCCC-CCCeeEEEEEEEEcCCCCEE
Q 032005 95 IAAGD-FVLSHTQTLPSF-TPPGSYTLKMTMEDKNNEEL 131 (149)
Q Consensus 95 l~~G~-~~~~~~~~ip~~-~P~g~~~v~~~l~d~~~~~~ 131 (149)
+++|+ ..+.+.+.+|.. ...+.-.+++++.|++++..
T Consensus 70 v~~g~~~~~~v~v~~p~~~~~~~~~~i~f~v~~~~~~~~ 108 (118)
T PF11614_consen 70 VPPGETREVPVFVTAPPDALKSGSTPITFTVTDDDGGEI 108 (118)
T ss_dssp E-TT-EEEEEEEEEE-GGG-SSSEEEEEEEEEEGGGTEE
T ss_pred ECCCCEEEEEEEEEECHHHccCCCeeEEEEEEECCCCEE
Confidence 77888 688888888855 45566688888875555443
No 89
>PF08139 LPAM_1: Prokaryotic membrane lipoprotein lipid attachment site; InterPro: IPR012640 In prokaryotes, membrane lipoproteins are synthesized with a precursor signal peptide, which is cleaved by a specific lipoprotein signal peptidase (signal peptidase II). The peptidase recognises a conserved sequence and cuts upstream of a cysteine residue to which a glyceride-fatty acid lipid is attached [,]. This lipid attachment site is found in homologues of the VirB proteins of type IV secretion systems (T4SS). Conjugal transfer across the cell envelope of Gram-negative bacteria is mediated by a supramolecular structure termed mating pair formation (Mpf) complex. Collectively, secretion pathways ancestrally related to bacterial conjugation systems are now known as T4SS. T4SS are involved in the delivery of effector molecules to eukaryotic target cells; each of these systems exports distinct DNA or protein substrates to effect a myriad of changes in host cell physiology during infection [].
Probab=36.42 E-value=15 Score=18.05 Aligned_cols=11 Identities=9% Similarity=0.301 Sum_probs=5.0
Q ss_pred cceehHHHHHH
Q 032005 2 DRQLMLFACFL 12 (149)
Q Consensus 2 ~~~~~l~~~~~ 12 (149)
-|.++++++++
T Consensus 8 Kkil~~l~a~~ 18 (25)
T PF08139_consen 8 KKILFPLLALF 18 (25)
T ss_pred HHHHHHHHHHH
Confidence 45444444443
No 90
>PRK06655 flgD flagellar basal body rod modification protein; Reviewed
Probab=36.25 E-value=62 Score=24.56 Aligned_cols=13 Identities=38% Similarity=0.761 Sum_probs=7.6
Q ss_pred CCCeeEEEEEEEE
Q 032005 112 TPPGSYTLKMTME 124 (149)
Q Consensus 112 ~P~g~~~v~~~l~ 124 (149)
+|+|.|++++...
T Consensus 167 lp~G~Yt~~V~A~ 179 (225)
T PRK06655 167 LPDGNYTIKASAS 179 (225)
T ss_pred CCCeeEEEEEEEE
Confidence 5556666666554
No 91
>PF10956 DUF2756: Protein of unknown function (DUF2756); InterPro: IPR020158 This entry contains proteins with no known function.
Probab=35.95 E-value=16 Score=24.16 Aligned_cols=24 Identities=25% Similarity=0.437 Sum_probs=15.7
Q ss_pred CcceehHHHHHHHhhhccCccceee
Q 032005 1 MDRQLMLFACFLLLVSSTQAIGVKY 25 (149)
Q Consensus 1 m~~~~~l~~~~~~~~~~~~~~~~~~ 25 (149)
|.|+ ++++++|.+++.|++++..+
T Consensus 1 MK~l-l~laalLPl~~~Aqp~n~~n 24 (104)
T PF10956_consen 1 MKRL-LILAALLPLAAMAQPLNTTN 24 (104)
T ss_pred ChHH-HHHHHHccHHHHHhHhhcCC
Confidence 6774 55666777777777655433
No 92
>PRK10965 multicopper oxidase; Provisional
Probab=34.96 E-value=62 Score=27.73 Aligned_cols=16 Identities=25% Similarity=0.173 Sum_probs=12.1
Q ss_pred CCCCCCCCe-EEEEEEE
Q 032005 91 VSCPIAAGD-FVLSHTQ 106 (149)
Q Consensus 91 ~~CPl~~G~-~~~~~~~ 106 (149)
..||+.||+ ++|.+..
T Consensus 116 pq~~I~PG~s~~Y~f~~ 132 (523)
T PRK10965 116 PQGIIAPGGKRTVTFTV 132 (523)
T ss_pred CCCCCCCCCEEEEEecc
Confidence 589999998 6665543
No 93
>PF13473 Cupredoxin_1: Cupredoxin-like domain; PDB: 1IBZ_D 1IC0_E 1IBY_D.
Probab=34.94 E-value=31 Score=22.30 Aligned_cols=28 Identities=21% Similarity=0.460 Sum_probs=14.4
Q ss_pred ccEEEeEEEEeCCC--CCCCCcEEEEEEEE
Q 032005 32 YAVTIQQVKIIPDP--VVTGKPATFNISAV 59 (149)
Q Consensus 32 ~~~~i~~~~i~Pc~--~~~G~~~~i~~~~~ 59 (149)
..+.+++-..+|-. +++|+++++++.-.
T Consensus 23 v~I~~~~~~f~P~~i~v~~G~~v~l~~~N~ 52 (104)
T PF13473_consen 23 VTITVTDFGFSPSTITVKAGQPVTLTFTNN 52 (104)
T ss_dssp -------EEEES-EEEEETTCEEEEEEEE-
T ss_pred ccccccCCeEecCEEEEcCCCeEEEEEEEC
Confidence 35667777888874 68899888776533
No 94
>cd02859 AMPKbeta_GBD_like AMP-activated protein kinase (AMPK) beta subunit glycogen binding domain (GBD). AMPK is a metabolic stress sensing protein that senses AMP/ATP and has recently been found to act as a glycogen sensor as well. The protein functions as a alpha-beta-gamma heterotrimer. This domain is the glycogen binding domain of the beta subunit.
Probab=34.37 E-value=1.1e+02 Score=18.74 Aligned_cols=12 Identities=8% Similarity=0.063 Sum_probs=7.3
Q ss_pred cEEEEEEEECCE
Q 032005 67 GKVVINVAYFGV 78 (149)
Q Consensus 67 ~~~~v~~~~~gi 78 (149)
..+.+...++++
T Consensus 13 ~~V~v~G~F~~W 24 (79)
T cd02859 13 KEVYVTGSFDNW 24 (79)
T ss_pred cEEEEEEEcCCC
Confidence 356666666664
No 95
>KOG1903 consensus Cell cycle-associated protein [Cell cycle control, cell division, chromosome partitioning]
Probab=33.70 E-value=14 Score=26.79 Aligned_cols=40 Identities=18% Similarity=0.370 Sum_probs=26.4
Q ss_pred cEEEEEEEECCEEeccC-CcCCCCCCCCCCCCCe--EEEEEEE
Q 032005 67 GKVVINVAYFGVPVHQE-TRDVCEEVSCPIAAGD--FVLSHTQ 106 (149)
Q Consensus 67 ~~~~v~~~~~gi~v~~~-~~d~C~~~~CPl~~G~--~~~~~~~ 106 (149)
..+++.=-++.+++.+. -.+.|...+||+-.|- |+|...-
T Consensus 61 ~AVHvVDFFNRiNLiYGTise~Cte~sCP~MsGG~rYEY~WqD 103 (217)
T KOG1903|consen 61 LAVHVVDFFNRINLIYGTISEFCTETSCPVMSGGPRYEYRWQD 103 (217)
T ss_pred eeeehhhhhhhhHhhhhhHhhhccccCCCcccCCCcceeEecc
Confidence 34444333556666555 4789999999999886 6665543
No 96
>KOG4824 consensus Apolipoprotein D/Lipocalin [Cell wall/membrane/envelope biogenesis]
Probab=33.60 E-value=19 Score=27.04 Aligned_cols=29 Identities=31% Similarity=0.395 Sum_probs=21.8
Q ss_pred CcceehHHHHHHHhhhccCccceeeCCCC
Q 032005 1 MDRQLMLFACFLLLVSSTQAIGVKYCDKK 29 (149)
Q Consensus 1 m~~~~~l~~~~~~~~~~~~~~~~~~C~~~ 29 (149)
|.++++.++++|+.++..|++.+.-|.+-
T Consensus 8 ~~~~~l~~~a~L~~~a~gqa~~lg~cpny 36 (224)
T KOG4824|consen 8 RKCFVLGFAAILLLSAAGQAIALGECPNY 36 (224)
T ss_pred HHHHHHHHHHHHHhhcccceEeeccCCCC
Confidence 34556666667777788899999999875
No 97
>PF00879 Defensin_propep: Defensin propeptide The pattern for this Prosite entry doesn't match the propeptide.; InterPro: IPR002366 Defensins are 2-6 kDa, cationic, microbicidal peptides active against many Gram-negative and Gram-positive bacteria, fungi, and enveloped viruses [], containing three pairs of intramolecular disulphide bonds []. On the basis of their size and pattern of disulphide bonding, mammalian defensins are classified into alpha, beta and theta categories. Alpha-defensins, which have been identified in humans, monkeys and several rodent species, are particularly abundant in neutrophils, certain macrophage populations and Paneth cells of the small intestine. Every mammalian species explored thus far has beta-defensins. In cows, as many as 13 beta-defensins exist in neutrophils. However, in other species, beta-defensins are more often produced by epithelial cells lining various organs (e.g. the epidermis, bronchial tree and genitourinary tract). Theta-defensins are cyclic and have so far only been identified in primate phagocytes. Defensins are produced constitutively and/or in response to microbial products or proinflammatory cytokines. Some defensins are also called corticostatins (CS) because they inhibit corticotropin-stimulated corticosteroid production. The mechanism(s) by which microorganisms are killed and/or inactivated by defensins is not understood completely. However, it is generally believed that killing is a consequence of disruption of the microbial membrane. The polar topology of defensins, with spatially separated charged and hydrophobic regions, allows them to insert themselves into the phospholipid membranes so that their hydrophobic regions are buried within the lipid membrane interior and their charged (mostly cationic) regions interact with anionic phospholipid head groups and water. Subsequently, some defensins can aggregate to form `channel-like' pores; others might bind to and cover the microbial membrane in a `carpet-like' manner. The net outcome is the disruption of membrane integrity and function, which ultimately leads to the lysis of microorganisms. Some defensins are synthesized as propeptides which may be relevant to this process - in neutrophils only the mature peptides have been identified but in Paneth cells, the propeptide is stored in vesicles [] and appears to be cleaved by trypsin on activation. ; GO: 0006952 defense response
Probab=33.23 E-value=25 Score=20.43 Aligned_cols=26 Identities=35% Similarity=0.374 Sum_probs=14.9
Q ss_pred ceehHHHHHHHhhhccCccceeeCCC
Q 032005 3 RQLMLFACFLLLVSSTQAIGVKYCDK 28 (149)
Q Consensus 3 ~~~~l~~~~~~~~~~~~~~~~~~C~~ 28 (149)
|.+.|+.++|+++-.+++-+......
T Consensus 2 RTL~LLaAlLLlAlqaQAepl~~~~d 27 (52)
T PF00879_consen 2 RTLALLAALLLLALQAQAEPLQERAD 27 (52)
T ss_pred cHHHHHHHHHHHHHHHhccccccccc
Confidence 55566666666665555555554443
No 98
>PF00801 PKD: PKD domain; InterPro: IPR000601 The PKD (Polycystic Kidney Disease) domain was first identified in the Polycystic Kidney Disease protein, polycystin-1 (PDK1 gene), and contains an Ig-like fold consisting of a beta-sandwich of seven strands in two sheets with a Greek key topology, although some members have additional strands []. Polycystin-1 is a large cell-surface glycoprotein involved in adhesive protein-protein and protein-carbohydrate interactions; however it is not clear if the PKD domain mediates any of these interactions. PKD domains are also found in other proteins, usually in the extracellular parts of proteins involved in interactions with other proteins. For example, domains with a PKD-type fold are found in archaeal surface layer proteins that protect the cell from extreme environments [], and in the human VPS10 domain-containing receptor SorCS2 [].; PDB: 1B4R_A 2KZW_A 2C4X_A 2C26_A 2Y72_B 3JQU_A 3JS7_B 1WGO_A 1L0Q_A.
Probab=32.52 E-value=57 Score=19.18 Aligned_cols=16 Identities=31% Similarity=0.713 Sum_probs=14.1
Q ss_pred CeeEEEEEEEEcCCCC
Q 032005 114 PGSYTLKMTMEDKNNE 129 (149)
Q Consensus 114 ~g~~~v~~~l~d~~~~ 129 (149)
+|.|+|+++..|+.|.
T Consensus 51 ~G~y~V~ltv~n~~g~ 66 (69)
T PF00801_consen 51 PGTYTVTLTVTNGVGS 66 (69)
T ss_dssp SEEEEEEEEEEETTSE
T ss_pred CeEEEEEEEEEECCCC
Confidence 6999999999998773
No 99
>PF12245 Big_3_2: Bacterial Ig-like domain (group 3); InterPro: IPR022038 This family of proteins is found in bacteria. They have two conserved sequence motifs: AGN and GMT.
Probab=32.00 E-value=83 Score=18.37 Aligned_cols=35 Identities=26% Similarity=0.311 Sum_probs=22.8
Q ss_pred EcCCCCCCeeEEEEEEEEcCCCCEEEEEEEEEEEcc
Q 032005 107 TLPSFTPPGSYTLKMTMEDKNNEELTCFSFNFKIGF 142 (149)
Q Consensus 107 ~ip~~~P~g~~~v~~~l~d~~~~~~~C~~~~v~i~~ 142 (149)
.+|..--.|.|+++++.+|.-|..-. ......+.+
T Consensus 15 ~~P~~~~dg~yt~~v~a~D~AGN~~~-~~~~~~i~d 49 (60)
T PF12245_consen 15 VIPENDADGEYTLTVTATDKAGNTSS-STTQIVIVD 49 (60)
T ss_pred cccCccCCccEEEEEEEEECCCCEEE-eeeEEEEEc
Confidence 35655456799999999998886532 344444443
No 100
>COG1952 SecB Preprotein translocase subunit SecB [Intracellular trafficking and secretion]
Probab=30.88 E-value=61 Score=23.26 Aligned_cols=27 Identities=19% Similarity=0.341 Sum_probs=17.6
Q ss_pred EEEEEEECCE-Ee---ccCCcCCCCCCCCCC
Q 032005 69 VVINVAYFGV-PV---HQETRDVCEEVSCPI 95 (149)
Q Consensus 69 ~~v~~~~~gi-~v---~~~~~d~C~~~~CPl 95 (149)
..+.+.++|+ .+ +...-..|-+..||-
T Consensus 76 F~~Ev~qaGvF~i~~i~~e~m~~~L~i~CP~ 106 (157)
T COG1952 76 FLCEVQQAGIFRIAGIPEEQMAHLLGIECPN 106 (157)
T ss_pred EEEEEEEeeEEEEcCCCHHHhhhhhhccCch
Confidence 3667778775 33 334567787788873
No 101
>PF10651 DUF2479: Domain of unknown function (DUF2479); InterPro: IPR018913 This domain is found in phage from a number of different bacteria including (Listeria phage A118 (Bacteriophage A118)). It is thought to be a putative long tail fibre protein.; PDB: 4DIV_L 3UH8_A.
Probab=30.72 E-value=1.2e+02 Score=21.61 Aligned_cols=44 Identities=9% Similarity=0.185 Sum_probs=25.5
Q ss_pred CCeEEEEEEEEcCCCCCCeeEEEEEEEEcC-CCCEEEEEEEEEEEcc
Q 032005 97 AGDFVLSHTQTLPSFTPPGSYTLKMTMEDK-NNEELTCFSFNFKIGF 142 (149)
Q Consensus 97 ~G~~~~~~~~~ip~~~P~g~~~v~~~l~d~-~~~~~~C~~~~v~i~~ 142 (149)
.|.++|..+-.+-+ -.|+++.++.+... +++.+.=.+|.+.|.+
T Consensus 81 ~G~i~y~lp~~~l~--~~G~v~a~~~i~~~~~~~~~~t~~F~F~V~~ 125 (170)
T PF10651_consen 81 NGIIQYTLPDEFLK--HVGKVKAQLFIYYNGDGQSISTANFTFEVED 125 (170)
T ss_dssp TTEEEEE--TTTTH--SSEEEEEEEEEEEESSSEEEE---EEEEEE-
T ss_pred CcEEEEEECHHHhc--cCcEEEEEEEEEECCCCCEEEEeeEEEEEec
Confidence 56666543333222 36999999888875 6767766667777776
No 102
>PLN02191 L-ascorbate oxidase
Probab=30.61 E-value=79 Score=27.45 Aligned_cols=16 Identities=31% Similarity=0.694 Sum_probs=12.5
Q ss_pred CCCCCCCCe-EEEEEEE
Q 032005 91 VSCPIAAGD-FVLSHTQ 106 (149)
Q Consensus 91 ~~CPl~~G~-~~~~~~~ 106 (149)
..||+.||+ ++|.+..
T Consensus 99 tq~pI~PG~s~~Y~f~~ 115 (574)
T PLN02191 99 TQCAINPGETFTYKFTV 115 (574)
T ss_pred ccCCcCCCCeEEEEEEC
Confidence 579999998 6776653
No 103
>PF03170 BcsB: Bacterial cellulose synthase subunit; InterPro: IPR018513 An operon encoding 4 proteins required for bacterial cellulose biosynthesis (bcs) in Acetobacter xylinus (Gluconacetobacter xylinus) has been isolated via genetic complementation with strains lacking cellulose synthase activity []. Nucleotide sequence analysis showed the cellulose synthase operon to consist of 4 genes, designated bcsA, bcsB, bcsC and bcsD, all of which are required for maximal bacterial cellulose synthesis in A. xylinum. The calculated molecular mass of the protein encoded by bcsB is 85.3kDa []. BcsB encodes the catalytic subunit of cellulose synthase. The protein polymerises uridine 5'-diphosphate glucose to cellulose: UDP-glucose + (1,4-beta-D-glucosyl)(N) = UDP + (1,4-beta-D-glucosyl)(N+1). The enzyme is specifically activated by the nucleotide cyclic diguanylic acid. Sequence analysis suggests that BcsB contains several transmembrane (TM) domains, and shares a high degree of similarity with Escherichia coli YhjN.; GO: 0006011 UDP-glucose metabolic process, 0016020 membrane
Probab=29.45 E-value=3.5e+02 Score=23.45 Aligned_cols=72 Identities=21% Similarity=0.293 Sum_probs=0.0
Q ss_pred CcEEEEEEEEeCeEecccEEEEEEEECCEEeccCCcCCCCCCCCCCCCCeE-EEEEEEEcCCCCCCeeEEEEEEEEcCCC
Q 032005 50 KPATFNISAVTGQAVYGGKVVINVAYFGVPVHQETRDVCEEVSCPIAAGDF-VLSHTQTLPSFTPPGSYTLKMTMEDKNN 128 (149)
Q Consensus 50 ~~~~i~~~~~~~~~i~~~~~~v~~~~~gi~v~~~~~d~C~~~~CPl~~G~~-~~~~~~~ip~~~P~g~~~v~~~l~d~~~ 128 (149)
+..++++.++....+....-++.+.+||..+-.. |+.+++- ..+.++.||+.+-.|.-++++++.....
T Consensus 44 ~~a~L~L~~~~S~~l~~~~S~L~V~lNg~~v~s~----------~l~~~~~~~~~~~i~Ip~~l~~g~N~l~~~~~~~~~ 113 (605)
T PF03170_consen 44 TKATLNLSYTYSPSLLPERSQLTVSLNGQPVGSI----------PLDAESAQPQTVTIPIPPALIKGFNRLTFEFIGHYT 113 (605)
T ss_pred cceEEEEEEEECcccCCCcceEEEEECCEEeEEE----------ecCcCCCCceEEEEecChhhcCCceEEEEEEEeccc
Q ss_pred CEEEE
Q 032005 129 EELTC 133 (149)
Q Consensus 129 ~~~~C 133 (149)
+. |
T Consensus 114 ~~--C 116 (605)
T PF03170_consen 114 DD--C 116 (605)
T ss_pred Cc--c
No 104
>PF02495 7kD_coat: 7kD viral coat protein; InterPro: IPR003411 This family consists of a 7 kDa coat protein from Carlavirus and Potexvirus [].
Probab=28.86 E-value=21 Score=20.98 Aligned_cols=7 Identities=14% Similarity=0.330 Sum_probs=3.7
Q ss_pred ccceeeC
Q 032005 20 AIGVKYC 26 (149)
Q Consensus 20 ~~~~~~C 26 (149)
...-++|
T Consensus 21 ~~~~~~C 27 (59)
T PF02495_consen 21 SPSSPSC 27 (59)
T ss_pred cCCCCCc
Confidence 3455556
No 105
>PF02018 CBM_4_9: Carbohydrate binding domain; InterPro: IPR003305 The 1,4-beta-glucanase CenC from Cellulomonas fimi contains two cellulose-binding domains, CBD(N1) and CBD(N2), arranged in tandem at its N terminus. These homologous CBDs are distinct in their selectivity for binding amorphous and not crystalline cellulose []. Multidimensional heteronuclear nuclear magnetic resonance (NMR) spectroscopy was used to determine the tertiary structure of the 152 amino acid N-terminal cellulose-binding domain from C. fimi 1,4-beta-glucanase CenC (CBDN1) []. The tertiary structure of CBDN1 is strikingly similar to that of the bacterial 1,3-1,4-beta-glucanases, as well as other sugar-binding proteins with jelly-roll folds.; GO: 0016798 hydrolase activity, acting on glycosyl bonds; PDB: 3OEA_B 2ZEX_B 3OEB_A 2ZEY_A 2ZEW_A 1GUI_A 2W5F_A 2WZE_A 2WYS_A 2ZEZ_B ....
Probab=28.14 E-value=1.3e+02 Score=19.44 Aligned_cols=31 Identities=16% Similarity=0.254 Sum_probs=15.9
Q ss_pred CCCCCCe-EEEEEEEEcCCCCCCeeEEEEEEEEcCCC
Q 032005 93 CPIAAGD-FVLSHTQTLPSFTPPGSYTLKMTMEDKNN 128 (149)
Q Consensus 93 CPl~~G~-~~~~~~~~ip~~~P~g~~~v~~~l~d~~~ 128 (149)
-++++|+ |++++.+..... ..+++.+.+.++
T Consensus 56 ~~l~~G~~Y~~s~~vk~~~~-----~~~~~~~~~~~~ 87 (131)
T PF02018_consen 56 ISLKPGKTYTVSFWVKADSG-----GTVSVSLRDEDG 87 (131)
T ss_dssp EEE-TTSEEEEEEEEEESSS-----EEEEEEEEESST
T ss_pred eEecCCCEEEEEEEEEeCCC-----CEEEEEEEEcCC
Confidence 4577777 666666655443 444444444433
No 106
>PRK15346 outer membrane secretin SsaC; Provisional
Probab=28.01 E-value=32 Score=29.22 Aligned_cols=25 Identities=28% Similarity=0.390 Sum_probs=17.1
Q ss_pred CcceehHHHHHHHhhh---ccCccceee
Q 032005 1 MDRQLMLFACFLLLVS---STQAIGVKY 25 (149)
Q Consensus 1 m~~~~~l~~~~~~~~~---~~~~~~~~~ 25 (149)
|.|+++|++++||+.+ ++.+..|+.
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~w~~ 28 (499)
T PRK15346 1 MKKLLILIFLFLLNTAKFAASKSIPWQG 28 (499)
T ss_pred CchhHHHHHHHHHhhhhhhccCCCCCCC
Confidence 7888888887777654 345566754
No 107
>PF11033 ComJ: Competence protein J (ComJ); InterPro: IPR020354 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. The proteins in this entry play a role in the competence of cells to be transformed. They inhibit the activity of the DNA-entry nuclease. DNA-entry nuclease inhibitor is a subunit of a 75 kDa protein complex, which governs binding and entry of donor DNA. The complex is a tetramer of two subunits of the DNA-entry nuclease and two subunits of a competence-specific protein ComJ. Only the complex is able to bind ds- and ss-DNA []. It is found in the plasma membrane.
Probab=27.81 E-value=1.2e+02 Score=20.89 Aligned_cols=15 Identities=33% Similarity=0.538 Sum_probs=10.8
Q ss_pred CCCCCCCCeEEEEEE
Q 032005 91 VSCPIAAGDFVLSHT 105 (149)
Q Consensus 91 ~~CPl~~G~~~~~~~ 105 (149)
..+|+.+|+|.+...
T Consensus 90 ~~~~ip~G~Y~Lv~~ 104 (125)
T PF11033_consen 90 LSFDIPKGDYQLVFQ 104 (125)
T ss_pred EEEecCCCcEEEEEE
Confidence 478888998765543
No 108
>cd03452 MaoC_C MaoC_C The C-terminal hot dog fold of the MaoC (monoamine oxidase C) dehydratase regulatory protein. Orthologs of MaoC include PaaZ [Escherichia coli] and PaaN [Pseudomonas putida], which are putative ring-opening enzymes involved in phenylacetic acid degradation. The C-terminal domain of MaoC has sequence similarity to (R)-specific enoyl-CoA hydratase,Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. MaoC also has an N-terminal PutA domain like that found in the E. coli PutA proline dehydrogenase and other members of the aldehyde dehydrogenase family.
Probab=27.50 E-value=2e+02 Score=19.54 Aligned_cols=48 Identities=17% Similarity=0.183 Sum_probs=27.0
Q ss_pred CCCCCCCe-EEEEEEEE-c-CCCCC-CeeEEEEEEEEcCCCCEEEEEEEEEE
Q 032005 92 SCPIAAGD-FVLSHTQT-L-PSFTP-PGSYTLKMTMEDKNNEELTCFSFNFK 139 (149)
Q Consensus 92 ~CPl~~G~-~~~~~~~~-i-p~~~P-~g~~~v~~~l~d~~~~~~~C~~~~v~ 139 (149)
.=|+.+|+ .+...++. + ++.=+ .+..+++.++.|++|+.+.=.+..+.
T Consensus 86 ~~PV~~GDtl~~~~~V~~~~~~~~~~~~~v~~~~~~~nq~g~~V~~~~~~~~ 137 (142)
T cd03452 86 LEPVYPGDTIQVRLTCKRKIPRDGQDYGVVRWDAEVTNQNGELVASYDILTL 137 (142)
T ss_pred CCCCCCCCEEEEEEEEEEEeecCCCCcEEEEEEEEEEecCCCEEEEEEehHe
Confidence 46788888 44444432 2 12111 14567788888888876544444333
No 109
>PRK10883 FtsI repressor; Provisional
Probab=27.41 E-value=1.1e+02 Score=25.72 Aligned_cols=17 Identities=0% Similarity=-0.082 Sum_probs=12.4
Q ss_pred CCCCCCCCCCe-EEEEEE
Q 032005 89 EEVSCPIAAGD-FVLSHT 105 (149)
Q Consensus 89 ~~~~CPl~~G~-~~~~~~ 105 (149)
++..+|+.||+ |+|.+.
T Consensus 114 ~g~~~~I~PG~~~~y~f~ 131 (471)
T PRK10883 114 GGPARMMSPNADWAPVLP 131 (471)
T ss_pred CCccccCCCCCeEEEEEe
Confidence 45779999998 666544
No 110
>PRK09619 flgD flagellar basal body rod modification protein; Reviewed
Probab=27.35 E-value=1.1e+02 Score=23.11 Aligned_cols=15 Identities=27% Similarity=0.434 Sum_probs=9.2
Q ss_pred CCCCeeEEEEEEEEc
Q 032005 111 FTPPGSYTLKMTMED 125 (149)
Q Consensus 111 ~~P~g~~~v~~~l~d 125 (149)
..|+|.|++++...|
T Consensus 159 ~lp~G~Y~~~V~a~~ 173 (218)
T PRK09619 159 GLQPGQYQLSVVSGS 173 (218)
T ss_pred CCCCceeEEEEEEeC
Confidence 366677776666443
No 111
>PRK15098 beta-D-glucoside glucohydrolase; Provisional
Probab=27.31 E-value=2.3e+02 Score=25.60 Aligned_cols=74 Identities=11% Similarity=0.135 Sum_probs=39.7
Q ss_pred cEEEeEEEEeCCCCCCCCcEEEEEEEEeCeEecccE-EEEEEEECCEEeccCCcCCCCCCCCCCCCCeE-EEEEEE
Q 032005 33 AVTIQQVKIIPDPVVTGKPATFNISAVTGQAVYGGK-VVINVAYFGVPVHQETRDVCEEVSCPIAAGDF-VLSHTQ 106 (149)
Q Consensus 33 ~~~i~~~~i~Pc~~~~G~~~~i~~~~~~~~~i~~~~-~~v~~~~~gi~v~~~~~d~C~~~~CPl~~G~~-~~~~~~ 106 (149)
.|+.++..+++.....+..++++++.+...+...-. +.+++..-.-.+..+...+....+--++||+. +.++++
T Consensus 650 ~F~ys~l~v~~~~~~~~~~i~v~v~V~NtG~~~G~EVvQlYv~~~~~~~~~P~k~L~gF~Kv~L~pGes~~V~~~l 725 (765)
T PRK15098 650 TFTVSDVKLSSPTMKRDGKVTASVTVTNTGKREGATVVQLYLQDVTASMSRPVKELKGFEKIMLKPGETQTVSFPI 725 (765)
T ss_pred cEEeeccEeccccccCCCeEEEEEEEEECCCCCccEEEEEeccCCCCCCCCHHHhccCceeEeECCCCeEEEEEee
Confidence 566777777654444567777877777777653332 23333211111222334556544445999983 444443
No 112
>PRK15191 fimbrial protein BcfF; Provisional
Probab=27.28 E-value=1.4e+02 Score=21.21 Aligned_cols=14 Identities=21% Similarity=0.268 Sum_probs=7.9
Q ss_pred CcceehHHHHHHHh
Q 032005 1 MDRQLMLFACFLLL 14 (149)
Q Consensus 1 m~~~~~l~~~~~~~ 14 (149)
|-|++++-++++++
T Consensus 1 ~~~~~~~~~~~~~~ 14 (172)
T PRK15191 1 MRNDILYGIGMLLA 14 (172)
T ss_pred CcceehhHHHHHhh
Confidence 77875555544443
No 113
>PLN03160 uncharacterized protein; Provisional
Probab=26.87 E-value=2.8e+02 Score=20.83 Aligned_cols=11 Identities=18% Similarity=0.250 Sum_probs=6.2
Q ss_pred EEEEEEECCEE
Q 032005 69 VVINVAYFGVP 79 (149)
Q Consensus 69 ~~v~~~~~gi~ 79 (149)
.++.+.|+|..
T Consensus 114 ~~~~v~Y~g~~ 124 (219)
T PLN03160 114 TTTTIYYGGTV 124 (219)
T ss_pred eEEEEEECCEE
Confidence 45556666643
No 114
>PF07760 DUF1616: Protein of unknown function (DUF1616); InterPro: IPR011674 This is a group of sequences from hypothetical archaeal proteins. The region in question is approximately 330 amino acid residues long.
Probab=26.82 E-value=3.1e+02 Score=21.38 Aligned_cols=93 Identities=16% Similarity=0.165 Sum_probs=52.4
Q ss_pred EeCCCCCCCCcEEEEEEEEeCeEecccEEEEEEEECCEEeccCCcCCCCC------CCCCCCCCe-EEEEEEEEcCCCCC
Q 032005 41 IIPDPVVTGKPATFNISAVTGQAVYGGKVVINVAYFGVPVHQETRDVCEE------VSCPIAAGD-FVLSHTQTLPSFTP 113 (149)
Q Consensus 41 i~Pc~~~~G~~~~i~~~~~~~~~i~~~~~~v~~~~~gi~v~~~~~d~C~~------~~CPl~~G~-~~~~~~~~ip~~~P 113 (149)
.-|-.+..|++.++.+.....+ .+.....+.+..++......+.+.+.. .. -+..|+ .+..+++.. ..+
T Consensus 182 ~Ypt~l~~ge~~~v~vgI~NhE-~~~~~Ytv~v~l~~~~~~~~~~~~~~~~~l~~~~~-~L~~n~t~~~~~~~~~--~~~ 257 (287)
T PF07760_consen 182 DYPTNLTSGEPGTVIVGIENHE-GRPENYTVVVVLQNVTWNPNNYNVMESTVLDRPIV-TLADNETWEQPYKFTP--FIT 257 (287)
T ss_pred cCCeeEEcCCcEEEEEEEEcCC-CCcEEEEEEEEEeccccccccccccchhcccceEE-EeCCCCeEEEEEEEEE--ecC
Confidence 3466688999998888766555 344444455544432221114555542 11 455555 444555444 455
Q ss_pred CeeEEEEEEEEcCC-CCEEEEEEEE
Q 032005 114 PGSYTLKMTMEDKN-NEELTCFSFN 137 (149)
Q Consensus 114 ~g~~~v~~~l~d~~-~~~~~C~~~~ 137 (149)
..+.++++.++.++ +.+....+..
T Consensus 258 ~~~~~l~~lLY~~~~~~~~ayr~~~ 282 (287)
T PF07760_consen 258 GENPRLEYLLYKGGVNSENAYRSLH 282 (287)
T ss_pred CCceEEEEEEEcCCCCcchheeEEE
Confidence 77789999999875 4444444433
No 115
>COG3009 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.67 E-value=2.6e+02 Score=20.73 Aligned_cols=50 Identities=12% Similarity=0.186 Sum_probs=31.5
Q ss_pred CCCCCCCCeEEEEEEEEcC--CCCCCee--EEEEEEEEcCCCCEEEEEEEEEEE
Q 032005 91 VSCPIAAGDFVLSHTQTLP--SFTPPGS--YTLKMTMEDKNNEELTCFSFNFKI 140 (149)
Q Consensus 91 ~~CPl~~G~~~~~~~~~ip--~~~P~g~--~~v~~~l~d~~~~~~~C~~~~v~i 140 (149)
.+=|..+|+-.|+.++.|- .--|.|+ +.++|++.+++|+.+.=-.|.+++
T Consensus 104 a~~p~~s~q~~~~l~vtv~rF~gry~g~a~i~g~W~L~~~~G~~~~~r~F~~e~ 157 (190)
T COG3009 104 APAPASSGQDLYKLNVTVQRFDGRYTGKAVISGEWRLLHDKGQPLINRPFHLEL 157 (190)
T ss_pred ecccCCCCcceEEEEEEEeeecCcccCceEEEEEEEEeccccCccccCceeeee
Confidence 3678888875455555554 3345665 467899999888755444454443
No 116
>KOG4680 consensus Uncharacterized conserved protein, contains ML domain [General function prediction only]
Probab=25.98 E-value=1.2e+02 Score=21.51 Aligned_cols=35 Identities=17% Similarity=0.337 Sum_probs=26.5
Q ss_pred CCCCCCCe-EEEEEEEEcCCCCCCeeEEEE-----EEEEcC
Q 032005 92 SCPIAAGD-FVLSHTQTLPSFTPPGSYTLK-----MTMEDK 126 (149)
Q Consensus 92 ~CPl~~G~-~~~~~~~~ip~~~P~g~~~v~-----~~l~d~ 126 (149)
+=|..+|+ -+++.+.+.-..+-.|+|.++ |.+.++
T Consensus 47 PnP~a~Ge~aTf~i~~ntg~tIs~Gk~VIeV~y~gi~ihse 87 (153)
T KOG4680|consen 47 PNPPARGENATFSISGNTGETISEGKYVIEVSYGGIRIHSE 87 (153)
T ss_pred CCCCCCCCccEEEEecccccEeeCCeEEEEEEEeeEEEeec
Confidence 56788898 688888888777888988765 455554
No 117
>cd03455 SAV4209 SAV4209 is a Streptomyces avermitilis protein with a hot dog fold that is similar to those of (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. The alpha- and gamma-proteobacterial members of this CD have, in addition to a hot dog fold, an N-terminal extension.
Probab=24.28 E-value=2.1e+02 Score=18.70 Aligned_cols=15 Identities=7% Similarity=0.204 Sum_probs=9.9
Q ss_pred eEEEEEEEEcCCCCE
Q 032005 116 SYTLKMTMEDKNNEE 130 (149)
Q Consensus 116 ~~~v~~~l~d~~~~~ 130 (149)
...++.+..|++|+.
T Consensus 100 ~v~~~~~~~nq~G~~ 114 (123)
T cd03455 100 VVTVELWARNSEGDH 114 (123)
T ss_pred EEEEEEEEEcCCCCE
Confidence 456667777777754
No 118
>PF10182 Flo11: Flo11 domain; InterPro: IPR018789 This presumed domain is found at the N terminus of the Saccharomyces cerevisiae (Baker's yeast) Flo11 protein.
Probab=23.93 E-value=2.7e+02 Score=19.70 Aligned_cols=30 Identities=13% Similarity=0.153 Sum_probs=19.7
Q ss_pred CccEEEeEEEEeCCCCCCCCcEEEEEEEEeCeEec
Q 032005 31 NYAVTIQQVKIIPDPVVTGKPATFNISAVTGQAVY 65 (149)
Q Consensus 31 ~~~~~i~~~~i~Pc~~~~G~~~~i~~~~~~~~~i~ 65 (149)
.+.+.|++++- ..+....|++.|+..+.+.
T Consensus 19 ~~~~~v~~V~~-----v~dn~Y~Vti~f~~~~si~ 48 (152)
T PF10182_consen 19 NASFDVSSVEW-----VGDNTYEVTINFQGDESIP 48 (152)
T ss_pred ceEEEEeEEEE-----ecCCeEEEEEEEEEccccc
Confidence 34667776653 2456688888888877653
No 119
>PRK13031 preprotein translocase subunit SecB; Provisional
Probab=23.78 E-value=1.4e+02 Score=21.30 Aligned_cols=45 Identities=13% Similarity=0.152 Sum_probs=25.1
Q ss_pred CcEEEEEEEEeCeEecccEE-EEEEEECCE-Ee---ccCCcCCCCCCCCC
Q 032005 50 KPATFNISAVTGQAVYGGKV-VINVAYFGV-PV---HQETRDVCEEVSCP 94 (149)
Q Consensus 50 ~~~~i~~~~~~~~~i~~~~~-~v~~~~~gi-~v---~~~~~d~C~~~~CP 94 (149)
....+.++.+.....+..++ .+.+.++|+ .+ |...-..+-+..||
T Consensus 53 ~~yEV~L~vtvta~~~~~t~FlvEv~qaGIF~i~nipee~~~~~L~i~CP 102 (149)
T PRK13031 53 NTYETVLTLEVKVENDGMVAFEAEVKQAGIFTVANMQEAQIEHAKKAFCP 102 (149)
T ss_pred CcEEEEEEEEEEEEeCCceEEEEEEeEeeEEEEcCCCHHHHHHHHhcCCc
Confidence 34555555555555555544 678888886 33 22233444456776
No 120
>PRK10626 hypothetical protein; Provisional
Probab=23.78 E-value=64 Score=24.83 Aligned_cols=34 Identities=26% Similarity=0.254 Sum_probs=17.6
Q ss_pred CcceehHHHHHHHhhhccCccceeeCCCCCCccEEE
Q 032005 1 MDRQLMLFACFLLLVSSTQAIGVKYCDKKKNYAVTI 36 (149)
Q Consensus 1 m~~~~~l~~~~~~~~~~~~~~~~~~C~~~~~~~~~i 36 (149)
|+|..++.++|+++++. +..-.+|.=...+.+.|
T Consensus 1 ~mrk~~l~~~L~l~s~~--a~A~~qC~V~l~~DV~I 34 (239)
T PRK10626 1 MMRKMLLAALLSLTAMQ--AQADYQCSVTPQDDVII 34 (239)
T ss_pred ChHHHHHHHHHHHHHHH--HHhccCCCCCCCCCeEE
Confidence 77776665544444433 34447896443333333
No 121
>PF06051 DUF928: Domain of Unknown Function (DUF928); InterPro: IPR010328 This is a family of uncharacterised bacterial proteins.
Probab=23.71 E-value=2e+02 Score=21.07 Aligned_cols=30 Identities=7% Similarity=0.098 Sum_probs=19.7
Q ss_pred CCCCCe-EEEEEEEEcCCCCCCeeEEEEEEE
Q 032005 94 PIAAGD-FVLSHTQTLPSFTPPGSYTLKMTM 123 (149)
Q Consensus 94 Pl~~G~-~~~~~~~~ip~~~P~g~~~v~~~l 123 (149)
|++.|+ |.|.+++.-...-|+....++-++
T Consensus 86 ~Le~gk~Y~W~~~l~Cd~~~~s~~~~v~G~I 116 (189)
T PF06051_consen 86 PLEVGKTYRWYFSLICDPQDRSDDIFVEGWI 116 (189)
T ss_pred CCCCCCeEEEEEEEEECCCCCCCCceEEEEE
Confidence 789998 888888776544555554444333
No 122
>COG5137 Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]
Probab=23.04 E-value=3.5e+02 Score=20.74 Aligned_cols=44 Identities=18% Similarity=0.392 Sum_probs=33.6
Q ss_pred cEEEeEEEEeCCCCCCCCcEEEEEEEEeCeEecccEEEEEEEECC
Q 032005 33 AVTIQQVKIIPDPVVTGKPATFNISAVTGQAVYGGKVVINVAYFG 77 (149)
Q Consensus 33 ~~~i~~~~i~Pc~~~~G~~~~i~~~~~~~~~i~~~~~~v~~~~~g 77 (149)
.+++.++.+...|-+-|.++.++++|.--..+... +.+.+.|.|
T Consensus 3 iv~llsi~VlnnpaKf~DPykFeitFeClE~lK~d-lEwkltYvg 46 (279)
T COG5137 3 IVKLLSIEVLNNPAKFGDPYKFEITFECLEELKCD-LEWKLTYVG 46 (279)
T ss_pred eeeeEEEEeecChhhcCCCeeeEEEEEEhhhhcCC-ceEEEEEee
Confidence 56788999999999999999999999987766433 344445544
No 123
>TIGR02738 TrbB type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB. This protein is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically the F-type system. This protein has been predicted to contain a thioredoxin fold, contains a conserved pair of cysteines and has been shown to function as a thiol disulfide isomerase by complementation of an Ecoli DsbA defect. The protein is believed to be involved in pilin assembly. The protein is closely related to TraF (TIGR02739) which is somewhat longer, lacks the cysteine motif and is apparently not functional as a disulfide bond isomerase.
Probab=23.02 E-value=42 Score=23.73 Aligned_cols=23 Identities=17% Similarity=0.283 Sum_probs=12.2
Q ss_pred CcceehHHHHHHHhhhccCccce
Q 032005 1 MDRQLMLFACFLLLVSSTQAIGV 23 (149)
Q Consensus 1 m~~~~~l~~~~~~~~~~~~~~~~ 23 (149)
|.|.++.+++++..++.++...|
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~ 23 (153)
T TIGR02738 1 MLRKLLIVLLLLAGLAQASTLDE 23 (153)
T ss_pred CchHHHHHHHHHHHHHhcccHHH
Confidence 78865554444444555554444
No 124
>PRK11627 hypothetical protein; Provisional
Probab=22.73 E-value=1.6e+02 Score=21.78 Aligned_cols=9 Identities=11% Similarity=0.264 Sum_probs=5.5
Q ss_pred CcceehHHH
Q 032005 1 MDRQLMLFA 9 (149)
Q Consensus 1 m~~~~~l~~ 9 (149)
|+|-++|.+
T Consensus 1 mlkklll~l 9 (192)
T PRK11627 1 MLKKILFPL 9 (192)
T ss_pred ChHHHHHHH
Confidence 777766533
No 125
>TIGR03000 plancto_dom_1 Planctomycetes uncharacterized domain TIGR03000. Domains described by this model are found, so far, only in the Planctomycetes (Pirellula sp. strain 1 and Gemmata obscuriglobus), in up to six proteins per genome, and may be duplicated within a protein. The function is unknown.
Probab=22.38 E-value=2.1e+02 Score=17.91 Aligned_cols=35 Identities=14% Similarity=0.118 Sum_probs=19.2
Q ss_pred CCCCCCCCe-EEEEEEEEcCCCCCCeeEEEEEEEEc
Q 032005 91 VSCPIAAGD-FVLSHTQTLPSFTPPGSYTLKMTMED 125 (149)
Q Consensus 91 ~~CPl~~G~-~~~~~~~~ip~~~P~g~~~v~~~l~d 125 (149)
..=||++|. |.|.....+-.-=+...-.-++.+..
T Consensus 32 ~T~~L~~G~~y~Y~v~a~~~~dG~~~t~~~~V~vrA 67 (75)
T TIGR03000 32 TTPPLEAGKEYEYTVTAEYDRDGRILTRTRTVVVRA 67 (75)
T ss_pred ECCCCCCCCEEEEEEEEEEecCCcEEEEEEEEEEcC
Confidence 355789998 77777766532213333344444443
No 126
>PRK09934 fimbrial-like adhesin protein SfmF; Provisional
Probab=22.02 E-value=1.5e+02 Score=21.06 Aligned_cols=14 Identities=36% Similarity=0.479 Sum_probs=7.5
Q ss_pred CcceehHHHHHHHh
Q 032005 1 MDRQLMLFACFLLL 14 (149)
Q Consensus 1 m~~~~~l~~~~~~~ 14 (149)
|.|+++.++.+++.
T Consensus 1 m~~~~~~~~~~~~~ 14 (171)
T PRK09934 1 MRRVFFACFCGLLW 14 (171)
T ss_pred ChhHHHHHHHHHhh
Confidence 77765554443333
No 127
>TIGR03786 strep_pil_rpt streptococcal pilin isopeptide linkage domain. This model describes a domain that occurs once in the major pilin of Streptococcus pyogenes, Spy0128, but in higher copy numbers in other streptococcal proteins. The domain occurs nine times in a surface-anchored protein of Bifidobacterium longum. All members of this family have LPXTG-type sortase target sequences. The S. pyogenes major pilin has been shown to undergo isopeptide bond cross-linking, mediated by sortases, that are critical to maintaining pilus structural integrity. One such Lys-to-Asn isopeptide bond is to a near-invariant Asn near the C-terminal end of this domain (column 81 of the seed alignment). A Glu in the S. pyogenes major pilin (column 25 of the seed alignment), invariant as Glu or Gln, is described as catalytic for isopeptide bond formation.
Probab=21.96 E-value=1.9e+02 Score=17.26 Aligned_cols=34 Identities=18% Similarity=0.259 Sum_probs=21.0
Q ss_pred CCCeEEEEEEEEcCCCCCC-----eeEEEEEEEEcC-CCCE
Q 032005 96 AAGDFVLSHTQTLPSFTPP-----GSYTLKMTMEDK-NNEE 130 (149)
Q Consensus 96 ~~G~~~~~~~~~ip~~~P~-----g~~~v~~~l~d~-~~~~ 130 (149)
++|.|+|+.+-.- ...|. ..|.+++...|+ +|+.
T Consensus 8 ~~G~Y~YtV~E~~-g~~~gvtYD~~~~~vtV~V~~~~~G~L 47 (64)
T TIGR03786 8 KVGTYTYTITEVK-GKEPGVTYDTTVHTVTVTVTDDEQGKL 47 (64)
T ss_pred CCeEEEEEEEEeC-CCCCCeEecCCEEEEEEEEEECCCCcE
Confidence 5788888777542 23333 356788888875 4433
No 128
>PF06280 DUF1034: Fn3-like domain (DUF1034); InterPro: IPR010435 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain of unknown function is present in bacterial and plant peptidases belonging to MEROPS peptidase family S8 (subfamily S8A subtilisin, clan SB). It is C-terminal to and adjacent to the S8 peptidase domain and can be found in conjunction with the PA (Protease associated) domain (IPR003137 from INTERPRO) and additionally in Gram-positive bacteria with the surface protein anchor domain (IPR001899 from INTERPRO).; GO: 0004252 serine-type endopeptidase activity, 0005618 cell wall, 0016020 membrane; PDB: 3EIF_A 1XF1_B.
Probab=21.84 E-value=1.7e+02 Score=19.08 Aligned_cols=35 Identities=29% Similarity=0.350 Sum_probs=23.3
Q ss_pred CCCCe-EEEEEEEEcCCCCCC--ee-EEEEEEEEcCCCC
Q 032005 95 IAAGD-FVLSHTQTLPSFTPP--GS-YTLKMTMEDKNNE 129 (149)
Q Consensus 95 l~~G~-~~~~~~~~ip~~~P~--g~-~~v~~~l~d~~~~ 129 (149)
+.||+ .+++.++.+|+.+.. +. |..-+.+.+.+++
T Consensus 66 V~ag~s~~v~vti~~p~~~~~~~~~~~eG~I~~~~~~~~ 104 (112)
T PF06280_consen 66 VPAGQSKTVTVTITPPSGLDASNGPFYEGFITFKSSDGE 104 (112)
T ss_dssp E-TTEEEEEEEEEE--GGGHHTT-EEEEEEEEEESSTTS
T ss_pred ECCCCEEEEEEEEEehhcCCcccCCEEEEEEEEEcCCCC
Confidence 78898 688999999875543 44 5777888877775
No 129
>PF07213 DAP10: DAP10 membrane protein; InterPro: IPR009861 This family consists of several mammalian DAP10 membrane proteins. In activated mouse natural killer (NK) cells, the NKG2D receptor associates with two intracellular adaptors, DAP10 and DAP12, which trigger phosphatidyl inositol 3 kinase (PI3K) and Syk family protein tyrosine kinases, respectively. It has been suggested that the DAP10-PI3K pathway is sufficient to initiate NKG2D-mediated killing of target cells [].
Probab=21.73 E-value=75 Score=20.12 Aligned_cols=19 Identities=32% Similarity=0.287 Sum_probs=8.2
Q ss_pred CcceehHHHHHHHhhhccC
Q 032005 1 MDRQLMLFACFLLLVSSTQ 19 (149)
Q Consensus 1 m~~~~~l~~~~~~~~~~~~ 19 (149)
|.+---+++++|+..+.+|
T Consensus 1 m~~pG~lLflLLL~VaAaq 19 (79)
T PF07213_consen 1 MTPPGHLLFLLLLPVAAAQ 19 (79)
T ss_pred CCCccccHHHHHHHHhhhc
Confidence 4444334444444444343
No 130
>PF07411 DUF1508: Domain of unknown function (DUF1508); InterPro: IPR010879 This domain is found in a family of proteins, which have no known function. Members of this family are often found as tandem repeats and in some cases represent the whole protein.; PDB: 3BID_H 2K49_A 2K8E_A 2K7I_A.
Probab=21.45 E-value=1.4e+02 Score=16.75 Aligned_cols=15 Identities=13% Similarity=0.401 Sum_probs=9.8
Q ss_pred EEEEEEEcCCCCEEE
Q 032005 118 TLKMTMEDKNNEELT 132 (149)
Q Consensus 118 ~v~~~l~d~~~~~~~ 132 (149)
+.+|.|++.+|+.++
T Consensus 5 ~~~f~L~a~ng~via 19 (49)
T PF07411_consen 5 QFRFRLKAGNGEVIA 19 (49)
T ss_dssp EEEEEEE-TTS-EEE
T ss_pred CEEEEEEcCCCCEEE
Confidence 346888888898776
No 131
>COG5294 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.11 E-value=1.4e+02 Score=20.14 Aligned_cols=37 Identities=19% Similarity=0.187 Sum_probs=18.6
Q ss_pred CcceehHHHHHHHhhhccCccceeeCC-CCCCccEEEeE
Q 032005 1 MDRQLMLFACFLLLVSSTQAIGVKYCD-KKKNYAVTIQQ 38 (149)
Q Consensus 1 m~~~~~l~~~~~~~~~~~~~~~~~~C~-~~~~~~~~i~~ 38 (149)
|-+.++.+++++++.. +....|.+=. ++....++++.
T Consensus 1 MKkil~~ilall~~ii-~a~~~~~~~~~d~fnpyvk~~~ 38 (113)
T COG5294 1 MKKILIGILALLLIII-GALFIFYNINYDRFNPYVKITD 38 (113)
T ss_pred CcchHHHHHHHHHHHH-hhheEEEecccCCCCceEEEec
Confidence 7777666666555532 2334555443 22223555553
No 132
>PRK15209 long polar fimbrial protein LpfA; Provisional
Probab=20.90 E-value=2.1e+02 Score=20.19 Aligned_cols=24 Identities=17% Similarity=0.171 Sum_probs=11.4
Q ss_pred cEEEe-EEEEeCCCCCCC-CcEEEEE
Q 032005 33 AVTIQ-QVKIIPDPVVTG-KPATFNI 56 (149)
Q Consensus 33 ~~~i~-~~~i~Pc~~~~G-~~~~i~~ 56 (149)
.++++ .+.-.||.+..+ ++.+|++
T Consensus 27 ~I~f~G~I~~~tC~v~~~~~~~~V~L 52 (174)
T PRK15209 27 TVKFTGEIVDAPCVVSTDSQNQEVVL 52 (174)
T ss_pred EEEEEEEEEcCcceEeCCCCceEEEc
Confidence 44554 334467765543 2334443
No 133
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=20.61 E-value=36 Score=23.81 Aligned_cols=14 Identities=36% Similarity=0.503 Sum_probs=8.3
Q ss_pred CcceehHHHHHHHh
Q 032005 1 MDRQLMLFACFLLL 14 (149)
Q Consensus 1 m~~~~~l~~~~~~~ 14 (149)
|.|+++++++|+++
T Consensus 1 ~~~~~~~~~~~~~~ 14 (141)
T PRK12618 1 MMRLVLLLLLLLLA 14 (141)
T ss_pred ChhHHHHHHHHhCC
Confidence 78876665544443
No 134
>TIGR02588 conserved hypothetical protein TIGR02588. The function of this protein is unknown. It is always found as part of a two-gene operon with TIGR02587, a protein that appears to span the membrane seven times. It is found in Nostoc sp. PCC 7120, Agrobacterium tumefaciens, Sinorhizobium meliloti, and Gloeobacter violaceus, so far, all of which are bacterial.
Probab=20.32 E-value=3e+02 Score=18.92 Aligned_cols=28 Identities=7% Similarity=0.205 Sum_probs=16.4
Q ss_pred eeEEEEEEEEcCCCCEEEEEEEEEEEcc
Q 032005 115 GSYTLKMTMEDKNNEELTCFSFNFKIGF 142 (149)
Q Consensus 115 g~~~v~~~l~d~~~~~~~C~~~~v~i~~ 142 (149)
|.|++.++++|..|+.-.=+++.-.+..
T Consensus 49 gqyyVpF~V~N~gg~TAasV~V~geL~~ 76 (122)
T TIGR02588 49 GQYYVPFAIHNLGGTTAAAVNIRGELRQ 76 (122)
T ss_pred CEEEEEEEEEeCCCcEEEEEEEEEEEcc
Confidence 4466666666665555555555555544
No 135
>PF14054 DUF4249: Domain of unknown function (DUF4249)
Probab=20.27 E-value=4e+02 Score=20.29 Aligned_cols=15 Identities=27% Similarity=0.392 Sum_probs=9.6
Q ss_pred CCCcEEEEEEEEeCe
Q 032005 48 TGKPATFNISAVTGQ 62 (149)
Q Consensus 48 ~G~~~~i~~~~~~~~ 62 (149)
.++...|+++-+.+-
T Consensus 37 ~~~~~~V~Ls~s~~~ 51 (298)
T PF14054_consen 37 PGDPQTVRLSRSVPY 51 (298)
T ss_pred CCCcEEEEEEEeecc
Confidence 466677776666555
Done!