Query psy88
Match_columns 75
No_of_seqs 156 out of 1278
Neff 8.2
Searched_HMMs 46136
Date Fri Aug 16 19:34:56 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy88.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/88hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07732 Cu-oxidase_3: Multico 100.0 5.6E-32 1.2E-36 159.0 6.3 73 2-75 25-99 (117)
2 PLN02835 oxidoreductase 100.0 9.6E-30 2.1E-34 178.8 9.2 73 1-75 58-132 (539)
3 PLN02168 copper ion binding / 100.0 1.5E-29 3.2E-34 178.0 9.0 73 1-75 55-129 (545)
4 PLN02792 oxidoreductase 100.0 2.1E-29 4.5E-34 177.1 8.7 73 1-75 45-119 (536)
5 PLN02354 copper ion binding / 100.0 1.6E-29 3.5E-34 178.1 8.1 73 1-75 56-130 (552)
6 TIGR03389 laccase laccase, pla 100.0 3.4E-29 7.4E-34 175.9 9.1 74 1-75 32-107 (539)
7 PLN00044 multi-copper oxidase- 100.0 3.3E-29 7.1E-34 177.6 8.9 73 1-75 58-132 (596)
8 PLN02991 oxidoreductase 100.0 3.2E-29 6.9E-34 176.3 8.4 73 1-75 57-131 (543)
9 TIGR03390 ascorbOXfungal L-asc 100.0 5.9E-29 1.3E-33 174.8 9.2 75 1-75 37-114 (538)
10 PLN02191 L-ascorbate oxidase 100.0 1.3E-28 2.9E-33 174.1 9.3 75 1-75 52-127 (574)
11 TIGR03388 ascorbase L-ascorbat 99.9 2.6E-27 5.6E-32 166.6 9.5 75 1-75 30-105 (541)
12 PLN02604 oxidoreductase 99.9 1.1E-26 2.4E-31 164.1 9.5 74 2-75 54-128 (566)
13 TIGR01480 copper_res_A copper- 99.9 8.3E-27 1.8E-31 165.3 8.8 72 1-75 74-146 (587)
14 KOG1263|consensus 99.9 9E-27 2E-31 164.2 8.9 73 1-75 57-131 (563)
15 PRK10965 multicopper oxidase; 99.9 3.4E-25 7.3E-30 155.5 8.7 69 1-75 75-145 (523)
16 PRK10883 FtsI repressor; Provi 99.9 5E-23 1.1E-27 143.2 8.9 69 1-75 75-145 (471)
17 TIGR02376 Cu_nitrite_red nitri 99.8 2.1E-20 4.6E-25 124.6 8.6 66 2-74 58-125 (311)
18 TIGR01480 copper_res_A copper- 99.8 2.9E-19 6.4E-24 127.0 7.9 71 3-75 499-572 (587)
19 COG2132 SufI Putative multicop 99.8 4.2E-19 9.1E-24 122.7 8.2 72 1-75 62-134 (451)
20 TIGR03095 rusti_cyanin rusticy 99.7 4.1E-17 8.9E-22 99.3 8.5 74 2-75 51-133 (148)
21 PF07731 Cu-oxidase_2: Multico 99.5 3E-14 6.6E-19 84.5 6.0 72 2-75 33-120 (138)
22 TIGR03096 nitroso_cyanin nitro 99.3 6.5E-12 1.4E-16 75.4 7.3 59 2-74 60-119 (135)
23 PLN02835 oxidoreductase 99.1 2.2E-10 4.7E-15 81.4 6.1 71 4-75 412-497 (539)
24 COG2132 SufI Putative multicop 99.0 1.4E-09 3.1E-14 75.6 6.5 71 3-75 357-434 (451)
25 TIGR03388 ascorbase L-ascorbat 99.0 1.7E-09 3.7E-14 76.8 6.6 72 4-75 417-509 (541)
26 TIGR03389 laccase laccase, pla 99.0 2.3E-09 5.1E-14 76.1 6.8 72 4-75 416-505 (539)
27 PLN02604 oxidoreductase 98.9 3.3E-09 7.1E-14 75.8 6.6 72 4-75 440-532 (566)
28 PLN02168 copper ion binding / 98.9 5.7E-09 1.2E-13 74.4 6.9 71 4-75 416-501 (545)
29 PLN02354 copper ion binding / 98.9 3.9E-09 8.5E-14 75.3 5.9 71 4-75 419-504 (552)
30 PF13473 Cupredoxin_1: Cupredo 98.9 1E-08 2.2E-13 58.7 6.4 59 2-74 34-93 (104)
31 PRK10965 multicopper oxidase; 98.8 9.8E-09 2.1E-13 72.9 6.2 70 4-75 427-508 (523)
32 PLN02991 oxidoreductase 98.8 1.2E-08 2.6E-13 72.7 6.4 71 4-75 411-496 (543)
33 PLN02792 oxidoreductase 98.8 1.8E-08 3.8E-13 71.8 6.5 71 4-75 404-489 (536)
34 PLN02191 L-ascorbate oxidase 98.8 2.5E-08 5.3E-13 71.5 7.2 72 4-75 440-532 (574)
35 TIGR03390 ascorbOXfungal L-asc 98.8 2.3E-08 5E-13 71.1 6.8 72 4-75 413-517 (538)
36 TIGR02656 cyanin_plasto plasto 98.7 1.4E-07 3E-12 53.7 7.7 67 2-73 16-84 (99)
37 PLN00044 multi-copper oxidase- 98.7 5.4E-08 1.2E-12 70.1 5.9 70 4-74 434-518 (596)
38 PRK02888 nitrous-oxide reducta 98.6 1.3E-07 2.9E-12 68.2 7.1 62 2-74 554-616 (635)
39 TIGR02657 amicyanin amicyanin. 98.6 5.9E-07 1.3E-11 49.6 7.4 62 2-74 10-71 (83)
40 TIGR02376 Cu_nitrite_red nitri 98.5 1.9E-07 4.1E-12 62.7 5.4 71 4-75 203-280 (311)
41 PRK02710 plastocyanin; Provisi 98.4 2.7E-06 5.9E-11 49.9 7.7 59 2-73 46-104 (119)
42 PF00394 Cu-oxidase: Multicopp 98.4 8.4E-07 1.8E-11 54.1 5.1 71 2-73 59-135 (159)
43 PRK10883 FtsI repressor; Provi 98.3 1.1E-06 2.5E-11 61.8 5.6 66 4-75 376-453 (471)
44 PF00127 Copper-bind: Copper b 98.3 1.8E-06 3.9E-11 49.0 4.8 68 2-73 16-84 (99)
45 KOG1263|consensus 98.1 6.4E-06 1.4E-10 59.2 5.8 72 4-75 431-521 (563)
46 TIGR03102 halo_cynanin halocya 98.0 0.0001 2.2E-09 43.3 7.8 60 2-73 41-100 (115)
47 TIGR02375 pseudoazurin pseudoa 97.8 0.0001 2.2E-09 43.4 5.5 58 2-73 14-72 (116)
48 COG3794 PetE Plastocyanin [Ene 97.6 0.00051 1.1E-08 41.1 7.0 60 2-73 53-112 (128)
49 PF00116 COX2: Cytochrome C ox 97.4 0.0016 3.4E-08 38.3 6.8 58 2-74 45-103 (120)
50 TIGR03094 sulfo_cyanin sulfocy 97.2 0.0055 1.2E-07 38.8 7.8 69 2-73 84-168 (195)
51 PF06525 SoxE: Sulfocyanin (So 97.1 0.0059 1.3E-07 38.9 8.0 71 2-73 85-169 (196)
52 COG4263 NosZ Nitrous oxide red 96.7 0.0034 7.3E-08 44.9 4.5 60 3-73 558-618 (637)
53 TIGR02695 azurin azurin. Azuri 96.7 0.015 3.3E-07 34.6 6.6 70 4-74 17-111 (125)
54 TIGR02866 CoxB cytochrome c ox 95.4 0.12 2.7E-06 32.7 6.8 57 3-74 117-174 (201)
55 PRK13202 ureB urease subunit b 95.1 0.13 2.9E-06 29.7 5.5 60 3-63 11-83 (104)
56 PRK13203 ureB urease subunit b 94.3 0.28 6E-06 28.3 5.6 60 3-63 11-82 (102)
57 TIGR00192 urease_beta urease, 94.3 0.28 6.2E-06 28.2 5.6 60 3-63 11-82 (101)
58 PF12690 BsuPI: Intracellular 93.9 0.34 7.4E-06 26.6 5.3 32 40-71 41-80 (82)
59 cd00407 Urease_beta Urease bet 93.9 0.42 9.2E-06 27.5 5.8 60 3-63 11-82 (101)
60 PRK10378 inactive ferrous ion 93.3 0.59 1.3E-05 32.6 6.8 60 2-73 43-103 (375)
61 PRK13201 ureB urease subunit b 93.0 0.6 1.3E-05 28.2 5.7 60 3-63 11-82 (136)
62 PRK13198 ureB urease subunit b 93.0 0.54 1.2E-05 29.0 5.5 60 3-63 39-110 (158)
63 PRK13205 ureB urease subunit b 92.9 0.57 1.2E-05 28.9 5.6 60 3-63 11-82 (162)
64 PRK13204 ureB urease subunit b 92.9 0.56 1.2E-05 29.0 5.5 60 3-63 34-105 (159)
65 COG4263 NosZ Nitrous oxide red 92.8 0.37 8E-06 34.9 5.2 60 3-73 548-608 (637)
66 COG1622 CyoA Heme/copper-type 89.8 2.9 6.4E-05 27.6 6.9 57 3-74 137-194 (247)
67 PRK13192 bifunctional urease s 89.4 2.1 4.5E-05 27.7 5.7 60 3-63 120-191 (208)
68 PF05938 Self-incomp_S1: Plant 88.7 3 6.4E-05 23.7 5.9 52 14-74 2-54 (110)
69 PF00699 Urease_beta: Urease b 88.6 0.64 1.4E-05 26.7 2.8 59 4-63 11-81 (100)
70 PF10989 DUF2808: Protein of u 87.6 0.89 1.9E-05 27.4 3.2 25 49-73 96-125 (146)
71 PRK13986 urease subunit alpha; 86.4 3.6 7.8E-05 26.9 5.6 59 4-63 117-187 (225)
72 COG4454 Uncharacterized copper 85.6 5.8 0.00013 24.6 6.0 67 2-73 62-140 (158)
73 COG0832 UreB Urea amidohydrola 85.1 5.3 0.00012 23.1 5.3 59 4-63 12-82 (106)
74 TIGR03079 CH4_NH3mon_ox_B meth 83.6 2.2 4.8E-05 29.9 3.9 21 43-63 331-351 (399)
75 PF04744 Monooxygenase_B: Mono 82.5 2.2 4.7E-05 29.9 3.5 15 49-63 318-332 (381)
76 PF05506 DUF756: Domain of unk 82.4 6.1 0.00013 21.6 5.7 46 10-63 19-64 (89)
77 cd00918 Der-p2_like Several gr 80.9 9 0.00019 22.5 6.3 57 6-63 23-86 (120)
78 PF10633 NPCBM_assoc: NPCBM-as 80.3 4.2 9E-05 21.6 3.5 20 51-70 45-70 (78)
79 MTH00047 COX2 cytochrome c oxi 79.1 14 0.0003 23.5 6.5 57 3-74 116-173 (194)
80 COG2967 ApaG Uncharacterized p 78.6 3.3 7.3E-05 24.6 3.0 48 14-63 33-86 (126)
81 MTH00140 COX2 cytochrome c oxi 77.4 17 0.00036 23.6 6.3 56 4-74 141-197 (228)
82 PF00386 C1q: C1q domain; Int 77.4 3.2 7E-05 23.9 2.7 18 3-20 91-108 (127)
83 PLN02303 urease 74.8 10 0.00022 29.3 5.3 59 4-63 142-212 (837)
84 PRK05461 apaG CO2+/MG2+ efflux 73.6 8.7 0.00019 22.9 3.9 15 49-63 73-87 (127)
85 PF09394 Inhibitor_I42: Chagas 73.6 11 0.00025 20.3 4.2 18 5-22 1-18 (92)
86 cd05468 pVHL von Hippel-Landau 72.6 14 0.00031 22.2 4.7 43 8-60 4-46 (141)
87 cd00916 Npc2_like Niemann-Pick 71.3 18 0.00039 21.1 5.5 58 6-63 25-90 (123)
88 MTH00098 COX2 cytochrome c oxi 71.2 25 0.00055 22.8 6.8 56 4-74 141-197 (227)
89 smart00110 C1Q Complement comp 68.7 6.1 0.00013 23.5 2.5 16 3-18 96-111 (135)
90 PF09962 DUF2196: Uncharacteri 65.7 6.1 0.00013 20.8 1.8 36 7-45 9-56 (62)
91 MTH00129 COX2 cytochrome c oxi 65.6 35 0.00075 22.2 6.8 56 4-74 141-197 (230)
92 MTH00051 COX2 cytochrome c oxi 65.1 36 0.00078 22.2 6.0 55 4-73 145-200 (234)
93 TIGR00008 infA translation ini 64.6 7.7 0.00017 20.7 2.1 16 4-19 42-57 (68)
94 TIGR03833 conserved hypothetic 63.2 8.2 0.00018 20.3 2.0 37 6-45 7-55 (62)
95 PRK12442 translation initiatio 62.7 8.6 0.00019 21.6 2.2 28 4-31 44-71 (87)
96 KOG4387|consensus 62.6 3.4 7.3E-05 26.3 0.6 30 5-35 71-100 (191)
97 KOG4063|consensus 61.3 35 0.00075 21.2 4.8 16 48-63 106-121 (158)
98 MTH00008 COX2 cytochrome c oxi 61.2 43 0.00092 21.8 6.7 55 4-73 141-196 (228)
99 COG0361 InfA Translation initi 60.9 9.9 0.00021 20.7 2.2 17 4-20 44-60 (75)
100 KOG2500|consensus 59.5 7.3 0.00016 25.7 1.7 18 4-21 149-166 (253)
101 COG1188 Ribosome-associated he 58.9 6.3 0.00014 22.7 1.2 17 6-22 48-64 (100)
102 PF12306 PixA: Inclusion body 58.4 42 0.00091 20.8 6.7 18 3-20 58-75 (172)
103 cd08058 MPN_euk_mb Mpr1p, Pad1 57.9 5.1 0.00011 23.0 0.8 7 69-75 69-75 (119)
104 PRK12791 flbT flagellar biosyn 57.4 9.7 0.00021 22.9 1.9 27 1-29 1-30 (131)
105 PF00927 Transglut_C: Transglu 57.2 7.3 0.00016 21.8 1.3 19 50-68 60-81 (107)
106 COG2880 Uncharacterized protei 55.0 11 0.00023 20.2 1.6 19 1-19 18-36 (67)
107 PF05688 DUF824: Salmonella re 54.6 14 0.00031 18.3 2.0 15 5-19 7-21 (47)
108 PF07653 SH3_2: Variant SH3 do 51.4 9.4 0.0002 18.8 1.0 15 2-16 13-27 (55)
109 cd00912 ML The ML (MD-2-relate 51.3 14 0.00031 21.3 1.9 16 48-63 78-93 (127)
110 cd04456 S1_IF1A_like S1_IF1A_l 50.4 19 0.00041 19.6 2.2 17 4-20 36-52 (78)
111 cd05793 S1_IF1A S1_IF1A: Trans 50.0 19 0.00042 19.5 2.2 17 4-20 36-52 (77)
112 TIGR01432 QOXA cytochrome aa3 49.9 66 0.0014 20.6 5.7 56 3-73 130-186 (217)
113 MTH00185 COX2 cytochrome c oxi 49.7 71 0.0015 20.8 6.6 56 4-74 141-197 (230)
114 PF01847 VHL: von Hippel-Linda 49.6 35 0.00075 21.2 3.5 45 7-61 9-53 (156)
115 PF05753 TRAP_beta: Translocon 49.2 65 0.0014 20.2 5.1 21 49-69 80-103 (181)
116 PRK09838 periplasmic copper-bi 49.1 26 0.00056 20.5 2.8 17 6-22 88-104 (115)
117 cd07700 IgV_CD8_beta Immunoglo 49.1 33 0.00072 19.0 3.2 27 5-31 1-27 (107)
118 PF14646 MYCBPAP: MYCBP-associ 48.7 63 0.0014 22.8 5.1 61 4-69 240-317 (426)
119 TIGR01433 CyoA cytochrome o ub 48.5 74 0.0016 20.7 5.9 56 3-73 139-195 (226)
120 PF14326 DUF4384: Domain of un 47.9 25 0.00054 18.9 2.5 16 7-22 3-18 (83)
121 PF04744 Monooxygenase_B: Mono 47.4 18 0.00039 25.5 2.2 34 40-73 71-107 (381)
122 PF00207 A2M: Alpha-2-macroglo 47.3 37 0.0008 18.4 3.1 19 4-22 63-83 (92)
123 cd08067 MPN_2A_DUB Mov34/MPN/P 47.0 8.8 0.00019 24.2 0.6 7 69-75 83-89 (187)
124 PRK00794 flbT flagellar biosyn 47.0 19 0.0004 21.7 2.0 29 1-32 2-33 (132)
125 smart00207 TNF Tumour necrosis 46.8 19 0.00042 20.8 2.0 16 4-19 92-107 (125)
126 PF02221 E1_DerP2_DerF2: ML do 45.8 16 0.00035 20.9 1.6 16 48-63 84-99 (134)
127 cd08068 MPN_BRCC36 Mov34/MPN/P 45.1 10 0.00023 25.0 0.8 8 68-75 92-99 (244)
128 smart00652 eIF1a eukaryotic tr 44.8 26 0.00056 19.2 2.2 17 4-20 41-57 (83)
129 COG4895 Uncharacterized conser 44.2 28 0.00061 18.0 2.1 37 7-46 9-57 (63)
130 PRK04012 translation initiatio 44.1 26 0.00056 20.0 2.2 16 4-19 57-72 (100)
131 PF04246 RseC_MucC: Positive r 43.7 14 0.0003 21.7 1.1 17 4-20 49-65 (135)
132 COG0186 RpsQ Ribosomal protein 43.6 16 0.00034 20.5 1.2 15 4-18 53-67 (87)
133 TIGR03396 PC_PLC phospholipase 42.3 1.6E+02 0.0034 22.7 7.0 46 10-63 604-649 (690)
134 PF01176 eIF-1a: Translation i 41.8 17 0.00036 18.8 1.1 15 4-18 39-53 (65)
135 PF14796 AP3B1_C: Clathrin-ada 41.7 82 0.0018 19.2 5.3 47 12-63 88-137 (145)
136 PF07705 CARDB: CARDB; InterP 41.3 25 0.00054 18.7 1.9 20 51-70 56-78 (101)
137 PF08234 Spindle_Spc25: Chromo 41.2 27 0.00058 18.5 1.9 18 5-22 1-18 (74)
138 cd00175 SNc Staphylococcal nuc 41.2 27 0.00059 19.9 2.1 65 6-73 1-78 (129)
139 smart00737 ML Domain involved 40.8 26 0.00056 19.8 1.9 15 49-63 71-85 (118)
140 cd00164 S1_like S1_like: Ribos 40.8 41 0.00089 15.9 2.5 16 6-21 41-56 (65)
141 PF02563 Poly_export: Polysacc 40.3 25 0.00054 18.8 1.7 20 3-22 9-28 (82)
142 PF04379 DUF525: Protein of un 39.9 17 0.00038 20.2 1.1 14 50-63 57-70 (90)
143 PF04014 Antitoxin-MazE: Antid 39.6 21 0.00045 17.1 1.2 15 6-20 20-34 (47)
144 PF08496 Peptidase_S49_N: Pept 39.1 35 0.00077 21.0 2.4 24 6-33 127-150 (155)
145 KOG1555|consensus 39.0 12 0.00026 25.8 0.4 8 68-75 118-125 (316)
146 cd04980 IgV_L_kappa Immunoglob 39.0 67 0.0015 17.5 3.7 29 2-30 7-35 (106)
147 PF11604 CusF_Ec: Copper bindi 38.9 28 0.00062 18.3 1.8 17 6-22 42-58 (70)
148 MTH00038 COX2 cytochrome c oxi 38.9 1.1E+02 0.0024 19.9 6.4 55 4-73 141-196 (229)
149 cd04983 IgV_TCR_alpha_like Imm 38.7 67 0.0015 17.4 4.0 28 2-30 5-32 (109)
150 cd05720 Ig_CD8_alpha Immunoglo 38.5 59 0.0013 17.9 3.2 24 6-30 2-25 (104)
151 cd08961 GH64-TLP-SF glycoside 38.5 95 0.0021 19.1 5.5 21 51-71 30-51 (153)
152 cd05737 Ig_Myomesin_like_C C-t 38.1 65 0.0014 17.1 3.7 28 2-30 8-35 (92)
153 PF01954 DUF104: Protein of un 37.9 21 0.00045 18.5 1.1 19 2-20 17-35 (60)
154 cd04462 S1_RNAPII_Rpb7 S1_RNAP 37.8 53 0.0011 18.0 2.8 18 4-21 53-70 (88)
155 PF12988 DUF3872: Domain of un 37.8 15 0.00032 22.4 0.6 18 1-18 38-55 (137)
156 PF14250 AbrB-like: AbrB-like 37.6 19 0.0004 19.5 0.9 15 5-19 51-65 (71)
157 PF00229 TNF: TNF(Tumour Necro 37.3 22 0.00047 20.3 1.3 15 4-18 93-107 (127)
158 PF03658 Ub-RnfH: RnfH family 37.1 22 0.00047 19.8 1.1 11 6-16 61-71 (84)
159 cd03696 selB_II selB_II: this 36.4 36 0.00077 18.0 1.9 15 6-20 56-70 (83)
160 COG5004 P2-like prophage tail 36.3 13 0.00028 19.8 0.2 14 1-14 1-14 (70)
161 TIGR03635 S17_bact 30S ribosom 36.2 23 0.00051 18.9 1.2 11 6-16 48-58 (71)
162 PF04151 PPC: Bacterial pre-pe 36.1 64 0.0014 16.4 5.9 18 4-21 6-23 (70)
163 PF00868 Transglut_N: Transglu 36.0 56 0.0012 18.9 2.8 16 3-18 25-40 (118)
164 PF07679 I-set: Immunoglobulin 35.8 67 0.0014 16.5 3.6 28 2-30 7-34 (90)
165 cd05708 S1_Rrp5_repeat_sc12 S1 35.7 53 0.0011 16.6 2.5 16 6-21 47-62 (77)
166 smart00232 JAB_MPN JAB/MPN dom 35.6 19 0.0004 20.5 0.8 7 69-75 80-86 (135)
167 PTZ00047 cytochrome c oxidase 35.5 1.1E+02 0.0025 19.1 6.7 23 52-74 107-130 (162)
168 cd00184 TNF Tumor Necrosis Fac 35.4 35 0.00077 20.0 2.0 16 4-19 106-121 (137)
169 cd07701 Ig1_Necl-3 First (N-te 35.1 79 0.0017 17.1 3.9 28 2-30 4-31 (95)
170 CHL00084 rpl19 ribosomal prote 35.0 34 0.00073 20.2 1.8 16 5-20 21-36 (117)
171 PRK05659 sulfur carrier protei 35.0 25 0.00054 17.8 1.1 13 4-16 48-60 (66)
172 smart00739 KOW KOW (Kyprides, 34.8 30 0.00065 14.1 1.2 10 7-16 2-11 (28)
173 COG1310 Predicted metal-depend 34.7 18 0.00039 21.1 0.6 8 68-75 72-79 (134)
174 TIGR01451 B_ant_repeat conserv 34.6 35 0.00076 16.9 1.6 17 52-68 8-25 (53)
175 TIGR01024 rplS_bact ribosomal 34.3 39 0.00085 19.8 2.0 17 5-21 17-33 (113)
176 PF03459 TOBE: TOBE domain; I 34.0 19 0.00042 17.9 0.6 14 6-19 46-59 (64)
177 PF14874 PapD-like: Flagellar- 33.5 84 0.0018 17.0 4.9 46 12-63 23-70 (102)
178 PF07385 DUF1498: Protein of u 33.5 1.1E+02 0.0024 20.2 4.1 50 5-61 112-167 (225)
179 KOG4680|consensus 33.5 43 0.00092 20.6 2.1 23 48-70 95-122 (153)
180 cd07767 MPN Mpr1p, Pad1p N-ter 33.3 21 0.00046 19.7 0.8 7 69-75 67-73 (116)
181 COG4013 Uncharacterized protei 33.2 32 0.00069 19.3 1.4 13 6-18 20-32 (91)
182 COG1917 Uncharacterized conser 33.0 59 0.0013 18.6 2.6 24 2-33 81-104 (131)
183 PF00018 SH3_1: SH3 domain; I 32.9 19 0.00041 17.1 0.4 14 3-16 12-25 (48)
184 cd03698 eRF3_II_like eRF3_II_l 32.8 43 0.00092 17.8 1.9 14 6-19 56-69 (83)
185 cd08066 MPN_AMSH_like Mov34/MP 32.8 21 0.00046 22.2 0.7 7 69-75 79-85 (173)
186 PRK11347 antitoxin ChpS; Provi 32.7 33 0.00072 18.8 1.4 16 5-20 24-39 (83)
187 PRK12281 rplX 50S ribosomal pr 32.7 30 0.00065 18.7 1.2 13 5-17 5-17 (76)
188 TIGR03000 plancto_dom_1 Planct 32.6 50 0.0011 18.0 2.1 16 48-63 32-47 (75)
189 CHL00142 rps17 ribosomal prote 32.6 25 0.00055 19.5 0.9 11 6-16 50-60 (84)
190 smart00318 SNc Staphylococcal 32.3 80 0.0017 18.1 3.2 33 3-38 6-38 (138)
191 cd05794 S1_EF-P_repeat_2 S1_EF 32.1 41 0.00089 17.2 1.6 13 4-16 35-47 (56)
192 PF01398 JAB: JAB1/Mov34/MPN/P 31.9 19 0.0004 20.2 0.4 6 69-74 85-90 (114)
193 cd08069 MPN_RPN11_CSN5 Mov34/M 31.8 22 0.00047 23.6 0.7 8 68-75 90-97 (268)
194 PHA03189 UL14 tegument protein 31.8 90 0.0019 21.8 3.6 18 52-69 128-148 (348)
195 PF07610 DUF1573: Protein of u 31.7 50 0.0011 15.7 1.8 42 15-62 2-43 (45)
196 PF14604 SH3_9: Variant SH3 do 31.6 30 0.00065 16.7 1.0 14 3-16 11-24 (49)
197 PLN00208 translation initiatio 31.5 46 0.001 20.4 2.0 17 4-20 68-84 (145)
198 PF11302 DUF3104: Protein of u 31.3 39 0.00084 18.4 1.5 20 2-21 1-20 (75)
199 PF11614 FixG_C: IG-like fold 31.1 88 0.0019 17.6 3.1 45 13-63 35-81 (118)
200 cd05689 S1_RPS1_repeat_ec4 S1_ 31.1 71 0.0015 16.1 2.5 16 6-21 48-63 (72)
201 PTZ00329 eukaryotic translatio 30.9 45 0.00097 20.7 1.9 16 4-19 68-83 (155)
202 cd05690 S1_RPS1_repeat_ec5 S1_ 30.6 75 0.0016 15.7 2.5 15 6-20 45-59 (69)
203 smart00205 THN Thaumatin famil 30.4 1.6E+02 0.0034 19.2 4.4 20 51-70 29-50 (218)
204 cd05891 Ig_M-protein_C C-termi 30.3 94 0.002 16.6 3.7 28 2-30 8-35 (92)
205 smart00326 SH3 Src homology 3 30.1 34 0.00073 15.9 1.1 17 3-19 17-33 (58)
206 PRK00276 infA translation init 30.0 54 0.0012 17.2 2.0 17 5-21 45-61 (72)
207 cd05688 S1_RPS1_repeat_ec3 S1_ 30.0 76 0.0017 15.4 2.6 15 6-20 44-58 (68)
208 PF03423 CBM_25: Carbohydrate 30.0 76 0.0016 17.3 2.6 24 10-34 1-27 (87)
209 cd04451 S1_IF1 S1_IF1: Transla 29.8 74 0.0016 16.1 2.4 14 6-19 40-53 (64)
210 PF06030 DUF916: Bacterial pro 29.8 1.2E+02 0.0026 17.6 3.7 14 50-63 87-100 (121)
211 KOG4792|consensus 29.7 34 0.00074 22.9 1.3 19 4-22 245-263 (293)
212 KOG4458|consensus 29.6 39 0.00084 18.1 1.3 28 2-30 9-36 (78)
213 PF05896 NQRA: Na(+)-transloca 29.5 44 0.00095 22.4 1.8 14 1-14 39-52 (257)
214 PRK05610 rpsQ 30S ribosomal pr 29.4 31 0.00067 19.1 0.9 11 6-16 53-63 (84)
215 PF01828 Peptidase_A4: Peptida 29.4 46 0.00099 21.4 1.9 18 5-22 89-106 (208)
216 MTH00023 COX2 cytochrome c oxi 29.3 1.7E+02 0.0037 19.2 6.3 56 4-74 152-208 (240)
217 cd04089 eRF3_II eRF3_II: domai 29.2 53 0.0011 17.4 1.9 14 6-19 55-68 (82)
218 PF08940 DUF1918: Domain of un 29.2 29 0.00064 18.0 0.8 12 5-16 1-12 (58)
219 PF13218 DUF4026: Protein of u 29.1 62 0.0013 22.4 2.5 25 50-74 147-179 (323)
220 cd04975 Ig4_SCFR_like Fourth i 29.1 1.1E+02 0.0024 16.9 3.4 27 3-30 11-38 (101)
221 PF09478 CBM49: Carbohydrate b 29.0 57 0.0012 17.4 2.0 13 51-63 66-78 (80)
222 cd05762 Ig8_MLCK Eighth immuno 29.0 1.1E+02 0.0023 16.7 4.1 28 2-30 7-34 (98)
223 CHL00141 rpl24 ribosomal prote 28.8 36 0.00077 18.7 1.1 15 4-18 6-20 (83)
224 PRK13855 type IV secretion sys 28.8 70 0.0015 22.7 2.8 21 2-22 336-356 (376)
225 PF08363 GbpC: Glucan-binding 28.7 72 0.0016 21.6 2.7 17 5-21 85-101 (283)
226 cd05899 IgV_TCR_beta Immunoglo 28.6 1.1E+02 0.0024 16.8 3.9 27 2-30 5-31 (110)
227 TIGR01003 PTS_HPr_family Phosp 28.4 32 0.0007 18.5 0.9 18 3-20 51-68 (82)
228 TIGR00523 eIF-1A eukaryotic/ar 28.3 56 0.0012 18.6 1.9 17 4-20 55-71 (99)
229 KOG1554|consensus 28.3 25 0.00055 24.2 0.6 8 68-75 134-141 (347)
230 PF00431 CUB: CUB domain CUB d 28.3 60 0.0013 17.3 2.0 17 4-20 30-46 (110)
231 COG2336 MazE Growth regulator 28.2 32 0.00069 19.1 0.8 17 4-20 23-39 (82)
232 cd00367 PTS-HPr_like Histidine 28.1 35 0.00075 17.9 1.0 18 3-20 47-64 (77)
233 PF00254 FKBP_C: FKBP-type pep 28.1 48 0.001 17.7 1.6 15 7-21 5-19 (94)
234 PRK05338 rplS 50S ribosomal pr 28.0 48 0.001 19.5 1.6 14 5-18 17-30 (116)
235 cd05685 S1_Tex S1_Tex: The C-t 28.0 58 0.0013 15.8 1.8 15 7-21 45-59 (68)
236 cd04472 S1_PNPase S1_PNPase: P 27.7 70 0.0015 15.6 2.1 14 7-20 45-58 (68)
237 KOG4795|consensus 27.7 58 0.0013 21.8 2.1 19 4-22 50-68 (264)
238 cd03693 EF1_alpha_II EF1_alpha 27.4 57 0.0012 17.7 1.8 14 6-19 60-73 (91)
239 TIGR01080 rplX_A_E ribosomal p 27.4 52 0.0011 19.3 1.7 13 4-16 39-51 (114)
240 PRK10525 cytochrome o ubiquino 27.4 2.1E+02 0.0046 19.7 6.0 56 3-73 151-207 (315)
241 PRK10850 PTS system phosphohis 27.4 34 0.00075 18.7 0.9 17 3-19 51-67 (85)
242 COG0335 RplS Ribosomal protein 27.0 51 0.0011 19.4 1.6 14 6-19 20-33 (115)
243 COG4118 Phd Antitoxin of toxin 27.0 24 0.00052 19.5 0.2 15 6-20 20-34 (84)
244 cd04452 S1_IF2_alpha S1_IF2_al 26.9 86 0.0019 15.8 2.4 15 7-21 50-64 (76)
245 cd05687 S1_RPS1_repeat_ec1_hs1 26.8 66 0.0014 16.1 1.9 15 7-21 45-59 (70)
246 cd05860 Ig4_SCFR Fourth immuno 26.7 95 0.0021 17.7 2.7 30 2-31 10-39 (101)
247 PF13533 Biotin_lipoyl_2: Biot 26.6 47 0.001 16.1 1.2 10 5-14 16-25 (50)
248 KOG1151|consensus 26.6 39 0.00085 25.2 1.3 21 52-72 622-647 (775)
249 TIGR03170 flgA_cterm flagella 26.6 86 0.0019 17.8 2.6 26 4-33 63-88 (122)
250 cd04471 S1_RNase_R S1_RNase_R: 26.5 96 0.0021 15.9 2.6 16 6-21 57-72 (83)
251 MTH00076 COX2 cytochrome c oxi 26.5 1.9E+02 0.0041 18.8 6.3 55 4-73 141-196 (228)
252 MTH00154 COX2 cytochrome c oxi 26.3 1.9E+02 0.0041 18.8 6.1 55 4-73 141-196 (227)
253 PF07452 CHRD: CHRD domain; I 26.3 1E+02 0.0022 17.3 2.8 18 14-32 38-55 (119)
254 TIGR02609 doc_partner putative 26.1 52 0.0011 17.4 1.5 16 5-20 22-37 (74)
255 PRK06518 hypothetical protein; 25.9 1.5E+02 0.0032 18.6 3.7 69 4-73 27-107 (177)
256 COG0198 RplX Ribosomal protein 25.9 55 0.0012 18.9 1.6 15 4-18 2-16 (104)
257 smart00841 Elong-fact-P_C Elon 25.9 54 0.0012 16.8 1.4 13 4-16 35-47 (56)
258 PF01557 FAA_hydrolase: Fumary 25.7 91 0.002 19.6 2.8 16 2-17 191-206 (218)
259 smart00316 S1 Ribosomal protei 25.7 92 0.002 14.9 2.5 16 6-21 46-61 (72)
260 PRK06944 sulfur carrier protei 25.5 39 0.00085 16.9 0.9 12 5-16 48-59 (65)
261 CHL00010 infA translation init 25.4 76 0.0017 17.0 2.1 16 5-20 45-60 (78)
262 cd00174 SH3 Src homology 3 dom 25.3 41 0.00089 15.4 0.9 15 4-18 15-29 (54)
263 PF01345 DUF11: Domain of unkn 25.2 60 0.0013 16.8 1.6 17 51-67 36-53 (76)
264 PRK10897 phosphohistidinoprote 25.2 37 0.0008 18.8 0.8 18 3-20 53-70 (90)
265 PTZ00241 40S ribosomal protein 25.1 37 0.0008 21.1 0.8 16 4-19 114-129 (158)
266 cd05686 S1_pNO40 S1_pNO40: pNO 25.0 93 0.002 15.9 2.3 15 7-21 49-63 (73)
267 PRK01191 rpl24p 50S ribosomal 24.8 64 0.0014 19.2 1.8 15 4-18 43-57 (120)
268 PRK05863 sulfur carrier protei 24.8 47 0.001 17.0 1.1 10 7-16 50-59 (65)
269 cd05705 S1_Rrp5_repeat_hs14 S1 24.7 60 0.0013 17.0 1.5 16 7-22 1-16 (74)
270 TIGR00638 Mop molybdenum-pteri 24.6 50 0.0011 16.5 1.2 15 5-19 47-61 (69)
271 TIGR01646 vgr_GE Rhs element V 24.4 96 0.0021 22.0 2.9 24 5-28 406-429 (483)
272 TIGR01683 thiS thiamine biosyn 24.4 62 0.0013 16.3 1.5 12 5-16 47-58 (64)
273 PF05489 Phage_tail_X: Phage T 24.4 35 0.00075 17.5 0.5 12 3-14 1-12 (60)
274 cd00565 ThiS ThiaminS ubiquiti 24.3 62 0.0013 16.4 1.5 12 5-16 48-59 (65)
275 COG3269 Predicted RNA-binding 24.3 61 0.0013 17.6 1.5 17 6-22 45-61 (73)
276 MTH00168 COX2 cytochrome c oxi 24.3 2.1E+02 0.0045 18.5 6.7 55 4-73 141-196 (225)
277 PF06205 GT36_AF: Glycosyltran 24.1 1.1E+02 0.0024 16.8 2.6 16 4-19 67-82 (90)
278 cd05716 Ig_pIgR Immunoglobulin 24.0 88 0.0019 16.7 2.2 14 4-17 1-14 (98)
279 PRK13831 conjugal transfer pro 24.0 99 0.0021 22.4 2.8 21 2-22 406-426 (432)
280 PRK13881 conjugal transfer pro 24.0 86 0.0019 22.9 2.5 21 2-22 442-462 (472)
281 PF11325 DUF3127: Domain of un 23.9 71 0.0015 17.7 1.7 14 6-19 52-65 (84)
282 cd03697 EFTU_II EFTU_II: Elong 23.8 77 0.0017 17.0 1.9 14 6-19 58-71 (87)
283 PF03712 Cu2_monoox_C: Copper 23.7 74 0.0016 19.3 2.0 16 3-18 85-100 (156)
284 COG2847 Copper(I)-binding prot 23.6 59 0.0013 20.1 1.5 15 4-18 113-127 (151)
285 PF09347 DUF1989: Domain of un 23.5 79 0.0017 19.6 2.1 13 4-16 11-23 (166)
286 PF10610 Tafi-CsgC: Thin aggre 23.5 93 0.002 18.1 2.2 18 3-20 71-88 (106)
287 TIGR00046 RNA methyltransferas 23.4 44 0.00095 21.6 1.0 14 4-17 29-42 (240)
288 TIGR03361 VI_Rhs_Vgr type VI s 23.3 96 0.0021 22.2 2.7 23 6-28 418-440 (513)
289 PRK10862 SoxR reducing system 23.3 37 0.00081 20.7 0.6 16 5-20 57-72 (154)
290 cd05692 S1_RPS1_repeat_hs4 S1_ 23.3 88 0.0019 15.1 2.0 14 7-20 45-58 (69)
291 PRK01777 hypothetical protein; 23.3 46 0.001 18.7 1.0 11 6-16 64-74 (95)
292 PF09285 Elong-fact-P_C: Elong 23.2 64 0.0014 16.5 1.4 11 6-16 37-47 (56)
293 PF11797 DUF3324: Protein of u 23.2 1E+02 0.0022 18.3 2.5 22 51-72 85-111 (140)
294 PRK09798 antitoxin MazE; Provi 23.0 61 0.0013 17.7 1.4 16 5-20 25-40 (82)
295 COG1596 Wza Periplasmic protei 22.9 92 0.002 20.2 2.4 19 3-21 44-62 (239)
296 cd05752 Ig1_FcgammaR_like Frst 22.8 90 0.0019 16.3 2.0 29 2-30 7-35 (78)
297 cd05691 S1_RPS1_repeat_ec6 S1_ 22.7 95 0.0021 15.4 2.1 15 7-21 45-59 (73)
298 cd05706 S1_Rrp5_repeat_sc10 S1 22.6 93 0.002 15.7 2.0 15 7-21 48-62 (73)
299 TIGR03027 pepcterm_export puta 22.4 69 0.0015 19.4 1.7 17 6-22 2-18 (165)
300 PRK08053 sulfur carrier protei 22.2 56 0.0012 16.7 1.1 12 5-16 49-60 (66)
301 cd05707 S1_Rrp5_repeat_sc11 S1 22.2 96 0.0021 15.4 2.0 16 7-22 45-60 (68)
302 cd04486 YhcR_OBF_like YhcR_OBF 22.2 59 0.0013 17.4 1.2 11 6-16 44-54 (78)
303 cd05696 S1_Rrp5_repeat_hs4 S1_ 22.1 93 0.002 15.9 2.0 16 7-22 47-62 (71)
304 cd05754 Ig3_Perlecan_like Thir 22.1 1.3E+02 0.0028 15.5 4.0 29 2-30 8-36 (85)
305 PF12790 T6SS-SciN: Type VI se 22.0 92 0.002 18.4 2.1 17 49-65 82-99 (142)
306 PF12945 YcgR_2: Flagellar pro 22.0 99 0.0022 16.1 2.1 60 7-72 1-68 (87)
307 PF13157 DUF3992: Protein of u 21.9 77 0.0017 17.9 1.7 13 51-63 57-69 (92)
308 cd09219 TLP-F thaumatin-like p 21.9 2.5E+02 0.0054 18.5 4.6 21 50-70 32-54 (229)
309 TIGR02756 TraK_Ftype type-F co 21.9 1.1E+02 0.0024 19.9 2.6 21 2-22 19-39 (232)
310 cd09218 TLP-PA allergenic/anti 21.8 2.4E+02 0.0052 18.4 4.4 22 50-71 30-52 (219)
311 cd05894 Ig_C5_MyBP-C C5 immuno 21.8 1.4E+02 0.0031 15.7 3.8 27 3-30 3-29 (86)
312 PRK00004 rplX 50S ribosomal pr 21.8 59 0.0013 18.6 1.2 15 5-19 3-17 (105)
313 smart00042 CUB Domain first fo 21.8 86 0.0019 16.5 1.9 16 4-19 21-36 (102)
314 cd05698 S1_Rrp5_repeat_hs6_sc5 21.7 1E+02 0.0022 15.4 2.0 15 7-21 45-59 (70)
315 PRK06488 sulfur carrier protei 21.7 59 0.0013 16.4 1.1 12 5-16 48-59 (65)
316 cd09215 Thaumatin-like the swe 21.7 2.1E+02 0.0046 17.6 4.6 21 50-70 28-49 (157)
317 PF13509 S1_2: S1 domain; PDB: 21.6 1.3E+02 0.0028 15.1 2.4 17 6-22 37-53 (61)
318 PF04225 OapA: Opacity-associa 21.4 50 0.0011 18.1 0.8 15 6-20 42-56 (85)
319 PF08206 OB_RNB: Ribonuclease 21.2 77 0.0017 15.8 1.5 13 7-19 32-44 (58)
320 PRK13782 phosphocarrier protei 21.2 50 0.0011 17.7 0.8 17 3-19 51-67 (82)
321 TIGR03630 arch_S17P archaeal r 21.1 56 0.0012 18.8 1.0 13 5-17 74-86 (102)
322 PF02933 CDC48_2: Cell divisio 21.1 1.1E+02 0.0023 15.4 2.0 14 5-18 17-30 (64)
323 cd05684 S1_DHX8_helicase S1_DH 21.0 1.3E+02 0.0028 15.5 2.4 15 6-20 48-62 (79)
324 PRK08572 rps17p 30S ribosomal 21.0 55 0.0012 19.1 0.9 13 5-17 76-88 (108)
325 cd00915 MD-1_MD-2 MD-1 and MD- 20.9 1.1E+02 0.0024 18.3 2.3 14 48-61 81-94 (130)
326 PF14801 GCD14_N: tRNA methylt 20.8 78 0.0017 16.2 1.4 10 7-16 6-15 (54)
327 cd00041 CUB CUB domain; extrac 20.8 1.1E+02 0.0024 16.2 2.2 17 4-20 31-47 (113)
328 cd00305 Cu-Zn_Superoxide_Dismu 20.6 2E+02 0.0044 17.0 3.5 24 10-34 26-49 (144)
329 cd05704 S1_Rrp5_repeat_hs13 S1 20.6 1E+02 0.0022 15.8 1.9 15 7-21 49-63 (72)
330 cd05695 S1_Rrp5_repeat_hs3 S1_ 20.5 1.1E+02 0.0023 15.5 2.0 17 6-22 42-58 (66)
331 PF04693 DDE_Tnp_2: Archaeal p 20.5 48 0.001 23.0 0.7 12 64-75 105-116 (327)
332 cd04454 S1_Rrp4_like S1_Rrp4_l 20.4 99 0.0021 16.1 1.9 16 7-22 51-66 (82)
333 PTZ00194 60S ribosomal protein 20.4 85 0.0018 19.2 1.7 16 4-19 44-59 (143)
334 cd08548 Type_I_cohesin_like Ty 20.3 1.3E+02 0.0029 17.7 2.6 15 4-18 7-21 (135)
335 PF00963 Cohesin: Cohesin doma 20.3 1.2E+02 0.0027 17.5 2.4 14 5-18 8-21 (141)
336 cd07690 Ig1_CD4 First immunogl 20.2 1.7E+02 0.0037 16.0 3.8 26 5-31 2-27 (94)
337 COG1278 CspC Cold shock protei 20.2 95 0.0021 16.5 1.7 17 6-22 41-57 (67)
338 cd05717 Ig1_Necl-1-3_like Firs 20.1 1.6E+02 0.0034 15.6 4.0 28 3-31 5-32 (95)
339 PRK13780 phosphocarrier protei 20.0 56 0.0012 18.0 0.8 18 3-20 51-68 (88)
340 cd05749 Ig2_Tyro3_like Second 20.0 1.6E+02 0.0034 15.6 3.6 29 2-30 5-33 (81)
No 1
>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=99.97 E-value=5.6e-32 Score=159.01 Aligned_cols=73 Identities=48% Similarity=0.865 Sum_probs=69.0
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CC-CeeeEEccCC
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-AN-AGTHFWHAHT 75 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~-~Gt~~YH~H~ 75 (75)
.++||+++||+|+|+|+|.++ .+++|||||+.++..+++||++..++++|.||++++|+|+ .+ +||||||||+
T Consensus 25 GPtI~v~~Gd~v~i~~~N~l~-~~~siH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~Y~~~~~~~~Gt~wYH~H~ 99 (117)
T PF07732_consen 25 GPTIRVREGDTVRITVTNNLD-EPTSIHWHGLHQPPSPWMDGVPGVTQCPIAPGESFTYEFTANQQAGTYWYHSHV 99 (117)
T ss_dssp EEEEEEETTEEEEEEEEEESS-SGBSEEEETSBSTTGGGGSGGTTTSGSSBSTTEEEEEEEEESSCSEEEEEEECS
T ss_pred CCEEEEEcCCeeEEEEEeccc-cccccccceeeeeeeeecCCcccccceeEEeecceeeeEeeeccccceeEeeCC
Confidence 579999999999999999998 8999999999998887899999999999999999999999 55 9999999995
No 2
>PLN02835 oxidoreductase
Probab=99.96 E-value=9.6e-30 Score=178.84 Aligned_cols=73 Identities=29% Similarity=0.559 Sum_probs=69.2
Q ss_pred CcccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc--CCCeeeEEccCC
Q psy88 1 MLYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT--ANAGTHFWHAHT 75 (75)
Q Consensus 1 ~~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~--~~~Gt~~YH~H~ 75 (75)
++++||+++||+|+|+++|+++ ++++|||||+.+...+|+||+++ +||||+||++|+|+|+ +++||||||||.
T Consensus 58 PGP~I~~~~GD~v~v~v~N~L~-~~ttiHWHGl~~~~~~~~DGv~~-tQ~pI~PG~sf~Y~F~~~~q~GT~WYHsH~ 132 (539)
T PLN02835 58 PGPRLDVVTNDNIILNLINKLD-QPFLLTWNGIKQRKNSWQDGVLG-TNCPIPPNSNYTYKFQTKDQIGTFTYFPST 132 (539)
T ss_pred CCCCEEEECCCEEEEEEEeCCC-CCCcEEeCCcccCCCCCCCCCcc-CcCCCCCCCcEEEEEEECCCCEeEEEEeCc
Confidence 4689999999999999999999 89999999999998889999998 8999999999999998 689999999994
No 3
>PLN02168 copper ion binding / pectinesterase
Probab=99.96 E-value=1.5e-29 Score=178.04 Aligned_cols=73 Identities=26% Similarity=0.501 Sum_probs=69.4
Q ss_pred CcccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc--CCCeeeEEccCC
Q psy88 1 MLYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT--ANAGTHFWHAHT 75 (75)
Q Consensus 1 ~~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~--~~~Gt~~YH~H~ 75 (75)
++++||+++||+|+|++.|+++ ++++|||||+.+...+|+||+++ +||||+||++|+|+|+ +++||||||||.
T Consensus 55 PGP~I~~~~GD~v~V~v~N~L~-~~ttiHWHGl~~~~~~~~DGv~g-tQcpI~PG~sftY~F~~~~q~GT~WYHsH~ 129 (545)
T PLN02168 55 PGPLLNATANDVINVNIFNNLT-EPFLMTWNGLQLRKNSWQDGVRG-TNCPILPGTNWTYRFQVKDQIGSYFYFPSL 129 (545)
T ss_pred CCCcEEEECCCEEEEEEEeCCC-CCccEeeCCccCCCCCCcCCCCC-CcCCCCCCCcEEEEEEeCCCCceEEEecCh
Confidence 4689999999999999999999 89999999999998889999999 9999999999999999 589999999994
No 4
>PLN02792 oxidoreductase
Probab=99.96 E-value=2.1e-29 Score=177.08 Aligned_cols=73 Identities=30% Similarity=0.598 Sum_probs=69.2
Q ss_pred CcccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc--CCCeeeEEccCC
Q psy88 1 MLYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT--ANAGTHFWHAHT 75 (75)
Q Consensus 1 ~~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~--~~~Gt~~YH~H~ 75 (75)
++++||+++||+|+|+|.|+++ ++++|||||+.++..+|+||+++ +||||+||++|+|+|+ +++||||||||.
T Consensus 45 PGP~I~~~~GD~v~V~v~N~L~-~~ttiHWHGl~q~~~~~~DGv~~-tqcPI~PG~sftY~F~~~~q~GT~WYHsH~ 119 (536)
T PLN02792 45 PGPEIRSLTNDNLVINVHNDLD-EPFLLSWNGVHMRKNSYQDGVYG-TTCPIPPGKNYTYDFQVKDQVGSYFYFPSL 119 (536)
T ss_pred CCCcEEEECCCEEEEEEEeCCC-CCcCEeCCCcccCCCCccCCCCC-CcCccCCCCcEEEEEEeCCCccceEEecCc
Confidence 4689999999999999999999 89999999999999899999987 8999999999999999 589999999995
No 5
>PLN02354 copper ion binding / oxidoreductase
Probab=99.96 E-value=1.6e-29 Score=178.06 Aligned_cols=73 Identities=34% Similarity=0.636 Sum_probs=69.5
Q ss_pred CcccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc--CCCeeeEEccCC
Q psy88 1 MLYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT--ANAGTHFWHAHT 75 (75)
Q Consensus 1 ~~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~--~~~Gt~~YH~H~ 75 (75)
++++||+++||+|+|++.|+++ ++++|||||+.+...+|+||+++ +||||+||++|+|+|+ +++||||||||.
T Consensus 56 PGP~I~~~~GD~v~V~v~N~l~-~~ttiHWHGi~q~~~~~~DGv~~-TQcpI~PG~sf~Y~F~~~~q~GT~WYHsH~ 130 (552)
T PLN02354 56 PGPNINSTSNNNIVINVFNNLD-EPFLLTWSGIQQRKNSWQDGVPG-TNCPIPPGTNFTYHFQPKDQIGSYFYYPST 130 (552)
T ss_pred cCCcEEEeCCCEEEEEEEECCC-CCcccccccccCCCCcccCCCcC-CcCCCCCCCcEEEEEEeCCCCcceEEecCc
Confidence 4689999999999999999998 89999999999998889999999 9999999999999999 589999999995
No 6
>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=99.96 E-value=3.4e-29 Score=175.94 Aligned_cols=74 Identities=42% Similarity=0.824 Sum_probs=70.3
Q ss_pred CcccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc--CCCeeeEEccCC
Q psy88 1 MLYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT--ANAGTHFWHAHT 75 (75)
Q Consensus 1 ~~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~--~~~Gt~~YH~H~ 75 (75)
++++|++++||+|+|+++|+++ .+++|||||+.+...+++||+++++||||+||++++|+|+ +++||||||||.
T Consensus 32 PGP~i~~~~GD~v~v~v~N~l~-~~tsiHwHGl~q~~~~~~DGv~~vTq~pI~PG~s~~Y~f~~~~~~GT~WYHsH~ 107 (539)
T TIGR03389 32 PGPTLYAREGDTVIVNVTNNVQ-YNVTIHWHGVRQLRNGWADGPAYITQCPIQPGQSYVYNFTITGQRGTLWWHAHI 107 (539)
T ss_pred cCCEEEEEcCCEEEEEEEeCCC-CCeeEecCCCCCCCCCCCCCCcccccCCcCCCCeEEEEEEecCCCeeEEEecCc
Confidence 4689999999999999999999 8999999999998888999999999999999999999999 599999999994
No 7
>PLN00044 multi-copper oxidase-related protein; Provisional
Probab=99.96 E-value=3.3e-29 Score=177.56 Aligned_cols=73 Identities=36% Similarity=0.604 Sum_probs=69.4
Q ss_pred CcccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc--CCCeeeEEccCC
Q psy88 1 MLYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT--ANAGTHFWHAHT 75 (75)
Q Consensus 1 ~~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~--~~~Gt~~YH~H~ 75 (75)
++++||+++||+|+|+|.|+++ .+++|||||+.+...+|+||+++ +||||+||++|+|+|+ +++||||||||+
T Consensus 58 PGPtI~~~~GD~v~V~V~N~L~-~~ttIHWHGl~q~~t~w~DGv~~-TQcPI~PG~sftY~F~~~dq~GT~WYHsH~ 132 (596)
T PLN00044 58 PGPALNVTTNWNLVVNVRNALD-EPLLLTWHGVQQRKSAWQDGVGG-TNCAIPAGWNWTYQFQVKDQVGSFFYAPST 132 (596)
T ss_pred CCCcEEEECCCEEEEEEEeCCC-CCccEEECCccCCCCccccCCCC-CcCCcCCCCcEEEEEEeCCCCceeEeeccc
Confidence 4689999999999999999999 89999999999999899999987 9999999999999999 699999999995
No 8
>PLN02991 oxidoreductase
Probab=99.96 E-value=3.2e-29 Score=176.30 Aligned_cols=73 Identities=26% Similarity=0.495 Sum_probs=69.1
Q ss_pred CcccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc--CCCeeeEEccCC
Q psy88 1 MLYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT--ANAGTHFWHAHT 75 (75)
Q Consensus 1 ~~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~--~~~Gt~~YH~H~ 75 (75)
++++|++++||+|+|+++|+++ ++++|||||+.+...+|+||+++ +||||+||++|+|+|+ +++||||||||.
T Consensus 57 PGP~I~~~~GD~v~V~V~N~L~-~~ttiHWHGi~q~~~~~~DGv~~-tQcpI~PG~sftY~F~~~~q~GT~WYHsH~ 131 (543)
T PLN02991 57 PGPDIISVTNDNLIINVFNHLD-EPFLISWSGIRNWRNSYQDGVYG-TTCPIPPGKNYTYALQVKDQIGSFYYFPSL 131 (543)
T ss_pred CCCcEEEECCCEEEEEecCCCC-CCccEEECCcccCCCccccCCCC-CCCccCCCCcEEEEEEeCCCCcceEEecCc
Confidence 4689999999999999999999 89999999999988889999988 8999999999999999 589999999994
No 9
>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=99.96 E-value=5.9e-29 Score=174.80 Aligned_cols=75 Identities=35% Similarity=0.666 Sum_probs=70.0
Q ss_pred CcccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc---CCCeeeEEccCC
Q psy88 1 MLYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT---ANAGTHFWHAHT 75 (75)
Q Consensus 1 ~~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~---~~~Gt~~YH~H~ 75 (75)
++++||+++||+|+|+|.|+++..+++|||||+.+...+|+||+++++||||+||++|+|+|+ +++||||||||.
T Consensus 37 PGP~I~~~~GD~v~V~v~N~L~~~~ttiHwHGi~~~~~~~~DGvp~vTQcpI~PG~sf~Y~f~~~~~q~GT~WYHsH~ 114 (538)
T TIGR03390 37 PGPEIRLQEGQTTWIRVYNDIPDNNVTMHWHGLTQRTAPFSDGTPLASQWPIPPGHFFDYEIKPEPGDAGSYFYHSHV 114 (538)
T ss_pred CCCeEEEeCCCEEEEEEEECCCCCCceEECCCCCCCCCCCCCCCcccccCCCCCCCcEEEEEEecCCCCeeeEEecCC
Confidence 468999999999999999998646899999999998888999999999999999999999998 389999999995
No 10
>PLN02191 L-ascorbate oxidase
Probab=99.96 E-value=1.3e-28 Score=174.06 Aligned_cols=75 Identities=43% Similarity=0.787 Sum_probs=70.7
Q ss_pred CcccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEccCC
Q psy88 1 MLYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHAHT 75 (75)
Q Consensus 1 ~~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~H~ 75 (75)
++++||+++||+|+|++.|+++..+++|||||+.+...+|+||+++++||||+||++|+|+|+ +++||||||||.
T Consensus 52 pGP~i~~~~Gd~v~v~v~N~l~~~~tsiHwHGl~~~~~~~~DGv~gvtq~pI~PG~s~~Y~f~~~~~GT~wYHsH~ 127 (574)
T PLN02191 52 PGPTIDAVAGDTIVVHLTNKLTTEGLVIHWHGIRQKGSPWADGAAGVTQCAINPGETFTYKFTVEKPGTHFYHGHY 127 (574)
T ss_pred CCCeEEEEcCCEEEEEEEECCCCCCccEECCCCCCCCCccccCCCccccCCcCCCCeEEEEEECCCCeEEEEeeCc
Confidence 468999999999999999998746899999999999888999999999999999999999999 999999999995
No 11
>TIGR03388 ascorbase L-ascorbate oxidase, plant type. Members of this protein family are the copper-containing enzyme L-ascorbate oxidase (EC 1.10.3.3), also called ascorbase. This family is found in flowering plants, and shows greater sequence similarity to a family of laccases (EC 1.10.3.2) from plants than to other known ascorbate oxidases.
Probab=99.95 E-value=2.6e-27 Score=166.58 Aligned_cols=75 Identities=41% Similarity=0.700 Sum_probs=70.0
Q ss_pred CcccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEccCC
Q psy88 1 MLYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHAHT 75 (75)
Q Consensus 1 ~~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~H~ 75 (75)
++++||+++||+|+|+|.|++...+++|||||+.+...+|+||+++++||+|+||++++|+|+ +++||||||||.
T Consensus 30 pGP~i~~~~Gd~v~v~v~N~l~~~~t~iHwHGl~~~~~~~~DG~~~vtq~~I~PG~s~~y~f~~~~~Gt~wyH~H~ 105 (541)
T TIGR03388 30 PGPTIRAQAGDTIVVELTNKLHTEGVVIHWHGIRQIGTPWADGTAGVTQCAINPGETFIYNFVVDRPGTYFYHGHY 105 (541)
T ss_pred CCCeEEEEcCCEEEEEEEECCCCCCccEEecCcCCcCCcccCCCCccccCCcCCCCEEEEEEEcCCCEEEEEEecc
Confidence 368999999999999999998546899999999988888899999999999999999999999 999999999994
No 12
>PLN02604 oxidoreductase
Probab=99.94 E-value=1.1e-26 Score=164.13 Aligned_cols=74 Identities=45% Similarity=0.730 Sum_probs=69.1
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEccCC
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHAHT 75 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~H~ 75 (75)
.++||+++||+|+|+|+|++..++++|||||+.+...+++||+++++||+|+||++++|+|+ +++||||||||.
T Consensus 54 gP~i~~~~Gd~v~v~v~N~l~~~~~~iH~HG~~~~~~~~~DG~~~~tq~~i~pg~s~~y~f~~~~~Gt~wyH~H~ 128 (566)
T PLN02604 54 GPTILAQQGDTVIVELKNSLLTENVAIHWHGIRQIGTPWFDGTEGVTQCPILPGETFTYEFVVDRPGTYLYHAHY 128 (566)
T ss_pred CCcEEEECCCEEEEEEEeCCCCCCCCEEeCCCCCCCCccccCCCccccCccCCCCeEEEEEEcCCCEEEEEeeCc
Confidence 57899999999999999998437899999999988778899999999999999999999999 999999999995
No 13
>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=99.94 E-value=8.3e-27 Score=165.26 Aligned_cols=72 Identities=38% Similarity=0.582 Sum_probs=67.6
Q ss_pred CcccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEccCC
Q psy88 1 MLYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHAHT 75 (75)
Q Consensus 1 ~~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~H~ 75 (75)
++++||+++||+|+|+|+|+++ .+++|||||+..+. .+||+|+++|++|+||++++|+|+ .++||||||||.
T Consensus 74 PGP~ir~~~Gd~v~v~v~N~l~-~~tsiHwHGl~~~~--~~DGvP~vt~~~I~PG~s~~Y~f~~~~~GTyWYHsH~ 146 (587)
T TIGR01480 74 PGPLLRWREGDTVRLRVTNTLP-EDTSIHWHGILLPF--QMDGVPGVSFAGIAPGETFTYRFPVRQSGTYWYHSHS 146 (587)
T ss_pred CCceEEEECCCEEEEEEEcCCC-CCceEEcCCCcCCc--cccCCCcccccccCCCCeEEEEEECCCCeeEEEecCc
Confidence 4689999999999999999999 89999999998864 589999999999999999999999 999999999995
No 14
>KOG1263|consensus
Probab=99.94 E-value=9e-27 Score=164.24 Aligned_cols=73 Identities=44% Similarity=0.830 Sum_probs=70.0
Q ss_pred CcccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc--CCCeeeEEccCC
Q psy88 1 MLYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT--ANAGTHFWHAHT 75 (75)
Q Consensus 1 ~~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~--~~~Gt~~YH~H~ 75 (75)
++++|++++||+|.|.+.|.++ ++.+|||||+++...+|+|| +.++||||+||++|+|+|+ ++.||||||+|+
T Consensus 57 PGP~I~~~~gD~ivV~v~N~~~-~~~sihWhGv~q~kn~w~DG-~~~TqCPI~Pg~~~tY~F~v~~q~GT~~yh~h~ 131 (563)
T KOG1263|consen 57 PGPTINAEEGDTIVVNVVNRLD-EPFSIHWHGVRQRKNPWQDG-VYITQCPIQPGENFTYRFTVKDQIGTLWYHSHV 131 (563)
T ss_pred CCCeEEEEeCCEEEEEEEeCCC-CceEEEeccccccCCccccC-CccccCCcCCCCeEEEEEEeCCcceeEEEeecc
Confidence 4689999999999999999999 89999999999999999999 9999999999999999999 699999999995
No 15
>PRK10965 multicopper oxidase; Provisional
Probab=99.92 E-value=3.4e-25 Score=155.54 Aligned_cols=69 Identities=35% Similarity=0.564 Sum_probs=63.1
Q ss_pred CcccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-C-CCeeeEEccCC
Q psy88 1 MLYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-A-NAGTHFWHAHT 75 (75)
Q Consensus 1 ~~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~-~~Gt~~YH~H~ 75 (75)
++++||+++||+|+|+++|.++ .+++|||||+.++. .+||+| ||+|+||++++|+|+ + ++||||||||.
T Consensus 75 PGPtIr~~~Gd~v~v~~~N~L~-~~ttiHwHGl~~~~--~~DG~p---q~~I~PG~s~~Y~f~~~q~aGT~WYH~H~ 145 (523)
T PRK10965 75 LGPAVRLQRGKAVTVDITNQLP-EETTLHWHGLEVPG--EVDGGP---QGIIAPGGKRTVTFTVDQPAATCWFHPHQ 145 (523)
T ss_pred CCceEEEECCCEEEEEEEECCC-CCccEEcccccCCC--ccCCCC---CCCCCCCCEEEEEeccCCCCceEEEecCC
Confidence 4689999999999999999999 89999999999875 389987 789999999999999 5 58999999994
No 16
>PRK10883 FtsI repressor; Provisional
Probab=99.89 E-value=5e-23 Score=143.21 Aligned_cols=69 Identities=20% Similarity=0.264 Sum_probs=60.0
Q ss_pred CcccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc--CCCeeeEEccCC
Q psy88 1 MLYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT--ANAGTHFWHAHT 75 (75)
Q Consensus 1 ~~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~--~~~Gt~~YH~H~ 75 (75)
++++||+++||+|+|++.|.++ ++++|||||+.++.. ..||++ ++|+||++++|.|+ +++||||||||.
T Consensus 75 pGPtir~~~Gd~v~v~v~N~L~-~~ttiHwHGl~~~~~-~~~g~~----~~I~PG~~~~y~f~~~~~aGT~WYH~H~ 145 (471)
T PRK10883 75 LGPTIRVWKGDDVKLIYSNRLT-EPVSMTVSGLQVPGP-LMGGPA----RMMSPNADWAPVLPIRQNAATCWYHANT 145 (471)
T ss_pred cCCeEEEECCCEEEEEEEeCCC-CCCceeECCccCCCC-CCCCcc----ccCCCCCeEEEEEecCCCceeeEEccCC
Confidence 3579999999999999999999 899999999998754 355543 46999999999998 569999999994
No 17
>TIGR02376 Cu_nitrite_red nitrite reductase, copper-containing. This family consists of copper-type nitrite reductase. It reduces nitrite to nitric oxide, the first step in denitrification.
Probab=99.83 E-value=2.1e-20 Score=124.60 Aligned_cols=66 Identities=23% Similarity=0.325 Sum_probs=57.0
Q ss_pred cccEEEecCCEEEEEEEeCCCC-CCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEccC
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDG-LENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHAH 74 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~-~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~H 74 (75)
.++||+++||+|+|+|+|.+.. .++++||||.. +.||.+..++ |+||++++|+|. +++||||||||
T Consensus 58 GP~irv~~Gd~v~v~v~N~~~~~~~h~~h~H~~~-----~~dg~~~~~~--I~PG~t~ty~F~~~~~Gty~YH~H 125 (311)
T TIGR02376 58 GPLIRVHEGDYVELTLINPPTNTMPHNVDFHAAT-----GALGGAALTQ--VNPGETATLRFKATRPGAFVYHCA 125 (311)
T ss_pred CceEEEECCCEEEEEEEeCCCCCCceeeeecCCC-----ccCCCCccee--ECCCCeEEEEEEcCCCEEEEEEcC
Confidence 5789999999999999999741 48999999963 3577766554 899999999999 99999999999
No 18
>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=99.79 E-value=2.9e-19 Score=127.03 Aligned_cols=71 Identities=21% Similarity=0.307 Sum_probs=59.7
Q ss_pred ccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCC--cccccccCCCCEEEEEEc-CCCeeeEEccCC
Q psy88 3 YPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVP--FVTQCPITQGNTFRYQFT-ANAGTHFWHAHT 75 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~--~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~H~ 75 (75)
.+|++++||+|+|+|.|.+. ++|+|||||+.+... ..||.. ...+..|+||++++|+|. +++|+||||||.
T Consensus 499 ~pl~v~~Gervri~l~N~t~-~~HpmHlHG~~f~v~-~~~G~~~~~~dTv~V~Pg~t~~~~f~ad~pG~w~~HCH~ 572 (587)
T TIGR01480 499 TPLRFNYGERLRVVLVNDTM-MAHPIHLHGMWSELE-DGQGEFQVRKHTVDVPPGGKRSFRVTADALGRWAYHCHM 572 (587)
T ss_pred CceEecCCCEEEEEEECCCC-CCcceeEcCceeeee-cCCCcccccCCceeeCCCCEEEEEEECCCCeEEEEcCCC
Confidence 47999999999999999998 899999999987643 235532 123467999999999999 999999999994
No 19
>COG2132 SufI Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=99.79 E-value=4.2e-19 Score=122.73 Aligned_cols=72 Identities=38% Similarity=0.604 Sum_probs=65.0
Q ss_pred CcccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEccCC
Q psy88 1 MLYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHAHT 75 (75)
Q Consensus 1 ~~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~H~ 75 (75)
+.++||+++||+|+|.++|.+. .++++||||+..+ ...||++..+++++.||++++|.|+ +.+||||||+|.
T Consensus 62 ~gP~i~~~~Gd~v~l~~~N~l~-~~t~vh~HG~~~p--~~~dG~~~~~~~~~~~~~~~~y~f~~~~~gT~wyh~H~ 134 (451)
T COG2132 62 PGPTIRVKKGDTVTLDLTNRLL-VDTSVHWHGLPVP--GEMDGVPPLTQIPPGPGETPTYTFTQDVPGTYWYHPHT 134 (451)
T ss_pred cCceEEEecCCEEEEEEEeCCC-CCceEEEcCcccC--ccccCCCcccccCCCCCCcEEEeecCCCCcceEeccCC
Confidence 3689999999999999999987 4599999998776 4589998888999999999999999 888899999995
No 20
>TIGR03095 rusti_cyanin rusticyanin. Rusticyanin is a blue copper protein, described in an obligate acidophilic chemolithoautroph, Acidithiobacillus ferrooxidans, as an electron transfer protein. It can constitute up to 5 percent of protein in cells grown on Fe(II) and is thought to be part of an electron chain for Fe(II) oxidation, with two c-type cytochromes, an aa3-type cytochrome oxidase, and 02 as terminal electron acceptor. It is rather closely related to sulfocyanin (TIGR03094).
Probab=99.72 E-value=4.1e-17 Score=99.29 Aligned_cols=74 Identities=19% Similarity=0.123 Sum_probs=55.9
Q ss_pred cccEEEecCCEEEEEEEeCCCC--CCceEEeCCccccCCCCCCCCCcccccccCCC----CE--EEEEEc-CCCeeeEEc
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDG--LENTIHWHGIHQRGTQYSDGVPFVTQCPITQG----NT--FRYQFT-ANAGTHFWH 72 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~--~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG----~~--~~y~~~-~~~Gt~~YH 72 (75)
.++|++++||+|+|.+.|..+. -...||++|...+..+.+||++..+++++.|+ +. .++.|+ .++|+||||
T Consensus 51 ~P~I~v~~Gd~V~v~v~N~~~~~~H~~~I~~~g~~~~~~p~mdG~~~~~~~~i~p~~~~g~~~~~~~tf~f~~aGtywyh 130 (148)
T TIGR03095 51 NPTIVIPEGVTVHFTVINTDTDSGHNFDISKRGPPYPYMPGMDGLGFVAGTGFLPPPKSGKFGYTDFTYHFSTAGTYWYL 130 (148)
T ss_pred CCEEEEcCCCEEEEEEEeCCCCccccEEeecCCCccccccccCCCCccccCcccCCCCCCccceeEEEEECCCCeEEEEE
Confidence 4678999999999999999641 23567777765554455899988888888773 22 355666 789999999
Q ss_pred cCC
Q psy88 73 AHT 75 (75)
Q Consensus 73 ~H~ 75 (75)
||.
T Consensus 131 C~~ 133 (148)
T TIGR03095 131 CTY 133 (148)
T ss_pred cCC
Confidence 984
No 21
>PF07731 Cu-oxidase_2: Multicopper oxidase; InterPro: IPR011706 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 2 domains.; GO: 0005507 copper ion binding, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3GDC_C 3ZX1_A 2YAH_A 2YAR_A 2YAQ_A 2YAO_A 2YAM_A 2YAF_A 2YAP_A 2XU9_A ....
Probab=99.52 E-value=3e-14 Score=84.54 Aligned_cols=72 Identities=22% Similarity=0.339 Sum_probs=58.5
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCc---------------ccccccCCCCEEEEEEc-CC
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPF---------------VTQCPITQGNTFRYQFT-AN 65 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~---------------~~~~~i~pG~~~~y~~~-~~ 65 (75)
...++++.|+.+++.+.|... .++++|+||..+.... .++... .....|+||+..+.+|. +.
T Consensus 33 ~~~~~~~~g~~v~~~l~N~~~-~~Hp~HlHG~~F~vl~-~~~~~~~~~~~~~~~~~~~~~~DTv~v~~~~~~~i~~~~~~ 110 (138)
T PF07731_consen 33 TPVIEVKNGDVVEIVLQNNGS-MPHPFHLHGHSFQVLG-RGGGPWNPDDTQSYNPENPGWRDTVLVPPGGWVVIRFRADN 110 (138)
T ss_dssp TSEEEEETTSEEEEEEEECTT-SSEEEEETTSEEEEEE-ETTEESTTHCGGCCCSSSSSEESEEEEETTEEEEEEEEETS
T ss_pred cceEEEeCCCEEEEEEECCCC-CccceEEEeeEEEeee-cCCcccccccccccccccCcccccccccceeEEEEEEEeec
Confidence 357899999999999999988 8999999998875332 222221 23566899999999999 99
Q ss_pred CeeeEEccCC
Q psy88 66 AGTHFWHAHT 75 (75)
Q Consensus 66 ~Gt~~YH~H~ 75 (75)
+|.|.||||.
T Consensus 111 ~G~w~~HCHi 120 (138)
T PF07731_consen 111 PGPWLFHCHI 120 (138)
T ss_dssp TEEEEEEESS
T ss_pred ceEEEEEEch
Confidence 9999999994
No 22
>TIGR03096 nitroso_cyanin nitrosocyanin. Nitrosocyanin, as described from the obligate chemolithoautotroph Nitrosomonas europaea, is a red copper protein of unknown function with sequence similarity to a number of blue copper redox proteins.
Probab=99.34 E-value=6.5e-12 Score=75.39 Aligned_cols=59 Identities=24% Similarity=0.253 Sum_probs=45.9
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEccC
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHAH 74 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~H 74 (75)
+..|++++||+|++++.|..+ .+ |++.... .|. ...++||++.+++|+ +++|+|+|||-
T Consensus 60 P~~I~VkaGD~Vtl~vtN~d~-~~-----H~f~i~~----~gi----s~~I~pGet~TitF~adKpG~Y~y~C~ 119 (135)
T TIGR03096 60 PEALVVKKGTPVKVTVENKSP-IS-----EGFSIDA----YGI----SEVIKAGETKTISFKADKAGAFTIWCQ 119 (135)
T ss_pred CCEEEECCCCEEEEEEEeCCC-Cc-----cceEECC----CCc----ceEECCCCeEEEEEECCCCEEEEEeCC
Confidence 568999999999999999876 44 4433321 122 224899999999999 99999999994
No 23
>PLN02835 oxidoreductase
Probab=99.10 E-value=2.2e-10 Score=81.43 Aligned_cols=71 Identities=13% Similarity=0.042 Sum_probs=55.5
Q ss_pred cEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCC--------------CCcccccccCCCCEEEEEEc-CCCee
Q psy88 4 PKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDG--------------VPFVTQCPITQGNTFRYQFT-ANAGT 68 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG--------------~~~~~~~~i~pG~~~~y~~~-~~~Gt 68 (75)
+++++.|+.|+|.+.|... .+|.||+||..+......+| .+...+..|++++....+|. ++||.
T Consensus 412 ~~~~~~~~~Veivi~N~~~-~~HP~HLHGh~F~Vlg~G~g~~~~~~~~~~nl~nP~~RDTv~vp~~gw~~IrF~aDNPG~ 490 (539)
T PLN02835 412 VMQTSLHDFLEVVFQNNEK-TMQSWHLDGYDFWVVGYGSGQWTPAKRSLYNLVDALTRHTAQVYPKSWTTILVSLDNQGM 490 (539)
T ss_pred EEEcCCCCEEEEEEECCCC-CCCCCCCCCccEEEEeccCCCCCcccccccCCCCCCccceEEeCCCCEEEEEEECcCCEE
Confidence 4677889999999999987 79999999988654322233 11123455788999999999 99999
Q ss_pred eEEccCC
Q psy88 69 HFWHAHT 75 (75)
Q Consensus 69 ~~YH~H~ 75 (75)
|++|||.
T Consensus 491 Wl~HCHi 497 (539)
T PLN02835 491 WNMRSAI 497 (539)
T ss_pred eeeeecc
Confidence 9999994
No 24
>COG2132 SufI Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=98.99 E-value=1.4e-09 Score=75.55 Aligned_cols=71 Identities=17% Similarity=0.264 Sum_probs=57.3
Q ss_pred ccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCC-----CC-CcccccccCCCCEEEEEEc-CCCeeeEEccCC
Q psy88 3 YPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSD-----GV-PFVTQCPITQGNTFRYQFT-ANAGTHFWHAHT 75 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~D-----G~-~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~H~ 75 (75)
.++.++.||..++.+.|... +.+.+|.||..+.... .| .. ..-....+.||++..++|. +.+|.|.||||.
T Consensus 357 ~~~~~~~G~~~~~~i~n~~~-~~HP~HlHg~~F~v~~-~~~~~~~~~~~~kDTv~v~~~~~~~v~~~a~~~g~~~~HCH~ 434 (451)
T COG2132 357 VTLIAKAGTRERWVLTNDTP-MPHPFHLHGHFFQVLS-GDAPAPGAAPGWKDTVLVAPGERLLVRFDADYPGPWMFHCHI 434 (451)
T ss_pred CceeecCCCEEEEEEECCCC-CccCeEEcCceEEEEe-cCCCcccccCccceEEEeCCCeEEEEEEeCCCCCceEEeccc
Confidence 57799999999999999998 8999999998876432 21 01 1112455899999999999 999999999994
No 25
>TIGR03388 ascorbase L-ascorbate oxidase, plant type. Members of this protein family are the copper-containing enzyme L-ascorbate oxidase (EC 1.10.3.3), also called ascorbase. This family is found in flowering plants, and shows greater sequence similarity to a family of laccases (EC 1.10.3.2) from plants than to other known ascorbate oxidases.
Probab=98.98 E-value=1.7e-09 Score=76.79 Aligned_cols=72 Identities=21% Similarity=0.212 Sum_probs=53.8
Q ss_pred cEEEecCCEEEEEEEeCCC-----CCCceEEeCCccccCCCCCCC---------------CCcccccccCCCCEEEEEEc
Q psy88 4 PKNVCEGDRVVVDVRNSMD-----GLENTIHWHGIHQRGTQYSDG---------------VPFVTQCPITQGNTFRYQFT 63 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~-----~~~~~iH~HG~~~~~~~~~DG---------------~~~~~~~~i~pG~~~~y~~~ 63 (75)
+++++.|+.|+|.|.|... ..+|.||+||..+.......| .+...+..|+|++....+|.
T Consensus 417 ~~~~~~g~~Vdivi~n~~~~~~~~~~~HP~HLHGh~F~vlg~g~g~~~~~~~~~~~n~~nP~~RDTv~vp~~gwvvIRF~ 496 (541)
T TIGR03388 417 IYRLKFNTTVDVILQNANTLNGNNSETHPWHLHGHDFWVLGYGEGKFRPGVDEKSYNLKNPPLRNTVVIFPYGWTALRFV 496 (541)
T ss_pred EEEecCCCeEEEEEECCccccCCCCCCCcEEecCCceEEEeeccCCCCcccCcccccCCCCCEeceEEeCCCceEEEEEE
Confidence 4788999999999999741 257999999987653321111 12223455789999999999
Q ss_pred -CCCeeeEEccCC
Q psy88 64 -ANAGTHFWHAHT 75 (75)
Q Consensus 64 -~~~Gt~~YH~H~ 75 (75)
++||.|++|||.
T Consensus 497 adNPG~W~~HCHi 509 (541)
T TIGR03388 497 ADNPGVWAFHCHI 509 (541)
T ss_pred CCCCeEeeeeccc
Confidence 999999999994
No 26
>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=98.96 E-value=2.3e-09 Score=76.06 Aligned_cols=72 Identities=19% Similarity=0.207 Sum_probs=54.1
Q ss_pred cEEEecCCEEEEEEEeCCC--CCCceEEeCCccccCCCCCCCC---------------CcccccccCCCCEEEEEEc-CC
Q psy88 4 PKNVCEGDRVVVDVRNSMD--GLENTIHWHGIHQRGTQYSDGV---------------PFVTQCPITQGNTFRYQFT-AN 65 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~--~~~~~iH~HG~~~~~~~~~DG~---------------~~~~~~~i~pG~~~~y~~~-~~ 65 (75)
+++++.|+.|+|.+.|... ..+|.||+||..+.......|. +...+..+++++....+|+ ++
T Consensus 416 v~~~~~~~~V~ivi~n~~~~~~~~HP~HLHGh~F~Vlg~g~g~~~~~~~~~~~nl~nP~rRDTv~vp~~g~vvirf~adN 495 (539)
T TIGR03389 416 VVRLKFNSTVELVLQDTSILGSENHPIHLHGYNFFVVGTGFGNFDPKKDPAKFNLVDPPERNTVGVPTGGWAAIRFVADN 495 (539)
T ss_pred EEEecCCCEEEEEEecCCcCCCCCCcEeEcCCceEEEEeccCCCCcccCccccccCCCCeeeeEEcCCCceEEEEEecCC
Confidence 4788999999999999742 1489999999876533222221 1112455789999999999 99
Q ss_pred CeeeEEccCC
Q psy88 66 AGTHFWHAHT 75 (75)
Q Consensus 66 ~Gt~~YH~H~ 75 (75)
||.|++|||.
T Consensus 496 PG~W~~HCHi 505 (539)
T TIGR03389 496 PGVWFMHCHL 505 (539)
T ss_pred CeEEEEEecc
Confidence 9999999994
No 27
>PLN02604 oxidoreductase
Probab=98.93 E-value=3.3e-09 Score=75.76 Aligned_cols=72 Identities=18% Similarity=0.214 Sum_probs=53.8
Q ss_pred cEEEecCCEEEEEEEeCCC-----CCCceEEeCCccccCCCCCCC---------------CCcccccccCCCCEEEEEEc
Q psy88 4 PKNVCEGDRVVVDVRNSMD-----GLENTIHWHGIHQRGTQYSDG---------------VPFVTQCPITQGNTFRYQFT 63 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~-----~~~~~iH~HG~~~~~~~~~DG---------------~~~~~~~~i~pG~~~~y~~~ 63 (75)
.++++.|+.|+|.|.|... ..+|.||+||..+.......| .+...+..|+|++....+|.
T Consensus 440 v~~~~~~~~Vdivi~n~~~~~~~~~~~HP~HLHGH~F~Vlg~G~G~~~~~~~~~~~nl~nP~rRDTv~vp~~gwvvIRF~ 519 (566)
T PLN02604 440 IYRLQFNSTVDIILQNANTMNANNSETHPWHLHGHDFWVLGYGEGKFNMSSDPKKYNLVDPIMKNTVPVHPYGWTALRFR 519 (566)
T ss_pred EEEccCCCeEEEEEECCccccCCCCCCCCEEecCCceEEEEecCCCCCccccccccCCCCCCccceEEeCCCceEEEEEE
Confidence 3788999999999999742 257999999987653321112 11123455789999999999
Q ss_pred -CCCeeeEEccCC
Q psy88 64 -ANAGTHFWHAHT 75 (75)
Q Consensus 64 -~~~Gt~~YH~H~ 75 (75)
++||.|++|||.
T Consensus 520 aDNPG~WlfHCHI 532 (566)
T PLN02604 520 ADNPGVWAFHCHI 532 (566)
T ss_pred CCCCeEeeEeecc
Confidence 999999999994
No 28
>PLN02168 copper ion binding / pectinesterase
Probab=98.90 E-value=5.7e-09 Score=74.40 Aligned_cols=71 Identities=11% Similarity=0.001 Sum_probs=54.4
Q ss_pred cEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCC--------------CCcccccccCCCCEEEEEEc-CCCee
Q psy88 4 PKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDG--------------VPFVTQCPITQGNTFRYQFT-ANAGT 68 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG--------------~~~~~~~~i~pG~~~~y~~~-~~~Gt 68 (75)
.++++.|+.|+|.+.|... .+|.||+||..+.......| .+...+..+++|+-...+|+ ++||.
T Consensus 416 v~~~~~~~~VeiViqn~~~-~~HP~HLHGh~F~Vvg~g~g~~~~~~~~~~Nl~nP~rRDTv~vp~~Gw~vIRF~aDNPG~ 494 (545)
T PLN02168 416 VVDIHYKDFYHIVFQNPLF-SLESYHIDGYNFFVVGYGFGAWSESKKAGYNLVDAVSRSTVQVYPYSWTAILIAMDNQGM 494 (545)
T ss_pred EEEecCCCEEEEEEeCCCC-CCCCeeeCCCceEEEECCCCCCCccccccCCCCCCCccceEEeCCCCEEEEEEEccCCeE
Confidence 3688999999999999876 79999999987653211111 11112445789999999999 99999
Q ss_pred eEEccCC
Q psy88 69 HFWHAHT 75 (75)
Q Consensus 69 ~~YH~H~ 75 (75)
|++|||.
T Consensus 495 Wl~HCHi 501 (545)
T PLN02168 495 WNVRSQK 501 (545)
T ss_pred EeeeecC
Confidence 9999993
No 29
>PLN02354 copper ion binding / oxidoreductase
Probab=98.89 E-value=3.9e-09 Score=75.27 Aligned_cols=71 Identities=14% Similarity=0.019 Sum_probs=54.5
Q ss_pred cEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCC--------------CCcccccccCCCCEEEEEEc-CCCee
Q psy88 4 PKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDG--------------VPFVTQCPITQGNTFRYQFT-ANAGT 68 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG--------------~~~~~~~~i~pG~~~~y~~~-~~~Gt 68 (75)
.++++.|+.|+|.+.|..+ .+|.||+||..+......+| .+...+..|++++-...+|+ ++||.
T Consensus 419 v~~~~~~~~VeiVi~n~~~-~~HP~HLHGh~F~Vlg~G~G~~~~~~~~~~nl~nP~rRDTv~vp~~Gw~vIRF~aDNPGv 497 (552)
T PLN02354 419 VLNITFRTFVEIIFENHEK-SMQSWHLDGYSFFAVAVEPGTWTPEKRKNYNLLDAVSRHTVQVYPKSWAAILLTFDNAGM 497 (552)
T ss_pred eEEcCCCCEEEEEEeCCCC-CCCCCcCCCccEEEEeecCCCCCccccccCCcCCCCccceEEeCCCCeEEEEEEecCCeE
Confidence 4677889999999999876 79999999988653322222 11112455788999999999 99999
Q ss_pred eEEccCC
Q psy88 69 HFWHAHT 75 (75)
Q Consensus 69 ~~YH~H~ 75 (75)
|++|||.
T Consensus 498 W~~HCHi 504 (552)
T PLN02354 498 WNIRSEN 504 (552)
T ss_pred Eeeeccc
Confidence 9999994
No 30
>PF13473 Cupredoxin_1: Cupredoxin-like domain; PDB: 1IBZ_D 1IC0_E 1IBY_D.
Probab=98.88 E-value=1e-08 Score=58.65 Aligned_cols=59 Identities=15% Similarity=0.109 Sum_probs=39.8
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEccC
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHAH 74 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~H 74 (75)
+..|+++.|+.++|++.|... .++.+..-++.. ...+.||++.++.|. +.+|+|-|+|-
T Consensus 34 P~~i~v~~G~~v~l~~~N~~~-~~h~~~i~~~~~-------------~~~l~~g~~~~~~f~~~~~G~y~~~C~ 93 (104)
T PF13473_consen 34 PSTITVKAGQPVTLTFTNNDS-RPHEFVIPDLGI-------------SKVLPPGETATVTFTPLKPGEYEFYCT 93 (104)
T ss_dssp S-EEEEETTCEEEEEEEE-SS-S-EEEEEGGGTE-------------EEEE-TT-EEEEEEEE-S-EEEEEB-S
T ss_pred cCEEEEcCCCeEEEEEEECCC-CcEEEEECCCce-------------EEEECCCCEEEEEEcCCCCEEEEEEcC
Confidence 568999999999999999977 565544433211 134899999999999 99999999994
No 31
>PRK10965 multicopper oxidase; Provisional
Probab=98.83 E-value=9.8e-09 Score=72.86 Aligned_cols=70 Identities=14% Similarity=0.088 Sum_probs=50.3
Q ss_pred cEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCc-------ccccccCCCCEEEEEEc-----CCCeeeEE
Q psy88 4 PKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPF-------VTQCPITQGNTFRYQFT-----ANAGTHFW 71 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~-------~~~~~i~pG~~~~y~~~-----~~~Gt~~Y 71 (75)
.++++.|++.+++|.|......|.+|+||..+.... .||.+. ..+..|+| ++.++.++ +..|.|.|
T Consensus 427 ~~~~~~G~~e~w~i~N~~~~~~Hp~HlHg~~F~Vl~-~~g~~~~~~~~~wkDTv~v~~-~~~~i~~~f~~~~~~~g~~~~ 504 (523)
T PRK10965 427 MFAAKKGQYERWVISGVGDMMLHPFHIHGTQFRILS-ENGKPPAAHRAGWKDTVRVEG-GRSEVLVKFDHDAPKEHAYMA 504 (523)
T ss_pred ceecCCCCEEEEEEEeCCCCCccCeEEeCcEEEEEE-ecCCCCCccccccccEEEECC-cEEEEEEEecCCCCCCCCEEE
Confidence 368999999999999997435899999999876542 455431 12344666 55555554 35679999
Q ss_pred ccCC
Q psy88 72 HAHT 75 (75)
Q Consensus 72 H~H~ 75 (75)
|||.
T Consensus 505 HCHi 508 (523)
T PRK10965 505 HCHL 508 (523)
T ss_pred EeCc
Confidence 9994
No 32
>PLN02991 oxidoreductase
Probab=98.82 E-value=1.2e-08 Score=72.73 Aligned_cols=71 Identities=13% Similarity=-0.033 Sum_probs=54.2
Q ss_pred cEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCC--------------CCcccccccCCCCEEEEEEc-CCCee
Q psy88 4 PKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDG--------------VPFVTQCPITQGNTFRYQFT-ANAGT 68 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG--------------~~~~~~~~i~pG~~~~y~~~-~~~Gt 68 (75)
.+.++.|+.|+|.|.|... .+|.||+||..+......+| .+...+..|++++....+|. ++||.
T Consensus 411 v~~~~~~~~VeiViqn~~~-~~HP~HLHGh~F~Vvg~G~G~f~~~~~~~~Nl~nP~rRDTv~vp~~Gw~vIRF~aDNPG~ 489 (543)
T PLN02991 411 VMQTDYKAFVEIVFENWED-IVQTWHLDGYSFYVVGMELGKWSAASRKVYNLNDAVSRCTVQVYPRSWTAIYVSLDNVGM 489 (543)
T ss_pred EEEcCCCCEEEEEEeCCCC-CCCCeeeCCcceEEEEeCCCCCCcccccccCCCCCCcccEEEECCCCEEEEEEECCCCEE
Confidence 3577889999999999877 79999999987653321111 11122455788999999999 99999
Q ss_pred eEEccCC
Q psy88 69 HFWHAHT 75 (75)
Q Consensus 69 ~~YH~H~ 75 (75)
|++|||.
T Consensus 490 W~~HCHi 496 (543)
T PLN02991 490 WNLRSEL 496 (543)
T ss_pred eeeeeCc
Confidence 9999994
No 33
>PLN02792 oxidoreductase
Probab=98.80 E-value=1.8e-08 Score=71.80 Aligned_cols=71 Identities=8% Similarity=0.012 Sum_probs=54.3
Q ss_pred cEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCC--------------CCcccccccCCCCEEEEEEc-CCCee
Q psy88 4 PKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDG--------------VPFVTQCPITQGNTFRYQFT-ANAGT 68 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG--------------~~~~~~~~i~pG~~~~y~~~-~~~Gt 68 (75)
.++++.|+.|+|.|.|... ..|++|+||..+......+| .+...+..|+|++-...+|. ++||.
T Consensus 404 v~~~~~~~~VeiViqn~~~-~~HP~HLHGh~F~Vvg~G~G~~~~~~~~~~Nl~nP~~RdTv~v~~~gw~aIRf~aDNPGv 482 (536)
T PLN02792 404 VMGAHHNAFLEIIFQNREK-IVQSYHLDGYNFWVVGINKGIWSRASRREYNLKDAISRSTTQVYPESWTAVYVALDNVGM 482 (536)
T ss_pred EEEcCCCCEEEEEEECCCC-CCCCeeeCCCceEEEeecCCCCCcccccccCcCCCCccceEEECCCCEEEEEEEeeCCEE
Confidence 4678899999999999866 68999999987653321122 11122455788999999999 99999
Q ss_pred eEEccCC
Q psy88 69 HFWHAHT 75 (75)
Q Consensus 69 ~~YH~H~ 75 (75)
|++|||.
T Consensus 483 W~~HCh~ 489 (536)
T PLN02792 483 WNLRSQF 489 (536)
T ss_pred EeeeEcc
Confidence 9999993
No 34
>PLN02191 L-ascorbate oxidase
Probab=98.79 E-value=2.5e-08 Score=71.50 Aligned_cols=72 Identities=22% Similarity=0.201 Sum_probs=53.1
Q ss_pred cEEEecCCEEEEEEEeCC-----CCCCceEEeCCccccCCCCCCC---------------CCcccccccCCCCEEEEEEc
Q psy88 4 PKNVCEGDRVVVDVRNSM-----DGLENTIHWHGIHQRGTQYSDG---------------VPFVTQCPITQGNTFRYQFT 63 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~-----~~~~~~iH~HG~~~~~~~~~DG---------------~~~~~~~~i~pG~~~~y~~~ 63 (75)
.++++.|+.|+|.|.|.. ...+|.||+||..+......+| .+...+..++|++....+|+
T Consensus 440 v~~~~~~~~Vdivi~n~~~~~~~~~~~HP~HLHGh~F~Vlg~G~g~~~~~~~~~~~nl~nP~rRDTv~vp~~Gw~vIRf~ 519 (574)
T PLN02191 440 IYVFPFNVTVDVIIQNANVLKGVVSEIHPWHLHGHDFWVLGYGDGKFKPGIDEKTYNLKNPPLRNTAILYPYGWTAIRFV 519 (574)
T ss_pred eEEecCCCEEEEEEECCCcccCCCCCCCCEEeCCCCeEEEEecCCCCCcccCcccccCCCCCcCCeEEeCCCCEEEEEEE
Confidence 356777999999999975 1268999999987653211122 11223455789999999999
Q ss_pred -CCCeeeEEccCC
Q psy88 64 -ANAGTHFWHAHT 75 (75)
Q Consensus 64 -~~~Gt~~YH~H~ 75 (75)
++||.|.+|||.
T Consensus 520 aDNPG~Wl~HCHi 532 (574)
T PLN02191 520 TDNPGVWFFHCHI 532 (574)
T ss_pred CCCCEEEEEecCc
Confidence 999999999994
No 35
>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=98.78 E-value=2.3e-08 Score=71.11 Aligned_cols=72 Identities=18% Similarity=0.206 Sum_probs=50.9
Q ss_pred cEEEecCCEEEEEEEeCC-------CCCCceEEeCCccccCCCCCCCC--------------C-ccccccc---------
Q psy88 4 PKNVCEGDRVVVDVRNSM-------DGLENTIHWHGIHQRGTQYSDGV--------------P-FVTQCPI--------- 52 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~-------~~~~~~iH~HG~~~~~~~~~DG~--------------~-~~~~~~i--------- 52 (75)
+++++.|+.|+|.|.|.. ...+|+||+||..+......+|. | ...+..+
T Consensus 413 ~~~~~~~~~V~ivi~n~~~~~~~~~~~~~HP~HlHGh~F~vlg~G~G~~~~~~~~~~~nl~nP~rRDTv~vp~~~~~~~~ 492 (538)
T TIGR03390 413 AFPAKVGEVLEIVWQNTGSYTGPNGGVDTHPFHAHGRHFYDIGGGDGEYNATANEAKLENYTPVLRDTTMLYRYAVKVVP 492 (538)
T ss_pred EEEcCCCCEEEEEEECCcccccCCCCCCCCCeeecCCcEEEEcccccccCCccChhhhccCCCCeecceeeccccccccc
Confidence 467899999999999974 12689999999775533222331 1 1112223
Q ss_pred -CCCCEEEEEEc-CCCeeeEEccCC
Q psy88 53 -TQGNTFRYQFT-ANAGTHFWHAHT 75 (75)
Q Consensus 53 -~pG~~~~y~~~-~~~Gt~~YH~H~ 75 (75)
.|+.....+|. ++||.|.+|||.
T Consensus 493 ~~~~~~~~ir~~~dNPG~W~~HCHi 517 (538)
T TIGR03390 493 GAPAGWRAWRIRVTNPGVWMMHCHI 517 (538)
T ss_pred cCCCceEEEEEEcCCCeeEEEeccc
Confidence 36778888899 999999999994
No 36
>TIGR02656 cyanin_plasto plastocyanin. Members of this family are plastocyanin, a blue copper protein related to pseudoazurin, halocyanin, amicyanin, etc. This protein, located in the thylakoid luman, performs electron transport to photosystem I in Cyanobacteria and chloroplasts.
Probab=98.73 E-value=1.4e-07 Score=53.73 Aligned_cols=67 Identities=12% Similarity=0.115 Sum_probs=42.9
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcc--cccccCCCCEEEEEEcCCCeeeEEcc
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFV--TQCPITQGNTFRYQFTANAGTHFWHA 73 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~--~~~~i~pG~~~~y~~~~~~Gt~~YH~ 73 (75)
+..|++++||+|+ ++|... .+|++.+.....+... .+..+.. +...+.||+++++.|.. +|+|.|+|
T Consensus 16 P~~i~v~~G~~V~--~~N~~~-~~H~~~~~~~~~~~~~-~~~~~~~~~~~~~~~pG~t~~~tF~~-~G~y~y~C 84 (99)
T TIGR02656 16 PAKISIAAGDTVE--WVNNKG-GPHNVVFDEDAVPAGV-KELAKSLSHKDLLNSPGESYEVTFST-PGTYTFYC 84 (99)
T ss_pred CCEEEECCCCEEE--EEECCC-CCceEEECCCCCccch-hhhcccccccccccCCCCEEEEEeCC-CEEEEEEc
Confidence 4679999999865 558765 6888776543222110 0000001 12246899999887775 89999999
No 37
>PLN00044 multi-copper oxidase-related protein; Provisional
Probab=98.67 E-value=5.4e-08 Score=70.08 Aligned_cols=70 Identities=13% Similarity=-0.045 Sum_probs=53.6
Q ss_pred cEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCC--------------CCcccccccCCCCEEEEEEc-CCCee
Q psy88 4 PKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDG--------------VPFVTQCPITQGNTFRYQFT-ANAGT 68 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG--------------~~~~~~~~i~pG~~~~y~~~-~~~Gt 68 (75)
.++++.++.|+|.|.|... .+|+||+||..+.......| .+...+..+++|+-...+|. ++||.
T Consensus 434 v~~~~~n~~VeiV~qn~~~-~~HP~HLHGh~F~Vvg~G~G~~~~~~~~~~Nl~nPp~RdTv~vp~~gW~aIRF~aDNPG~ 512 (596)
T PLN00044 434 IINGTYKGFMEIIFQNNAT-NVQSYHLDGYAFFVVGMDYGLWTDNSRGTYNKWDGVARSTIQVFPGAWTAILVFLDNAGI 512 (596)
T ss_pred EEEcCCCCEEEEEEeCCCC-CCCCeeEcCccEEEEeecCCCCCCCcccccccCCCCccceEEeCCCCeEEEEEecCCCEE
Confidence 3577889999999999865 69999999987653221121 11223455789999999999 99999
Q ss_pred eEEccC
Q psy88 69 HFWHAH 74 (75)
Q Consensus 69 ~~YH~H 74 (75)
|+.|||
T Consensus 513 W~lHCH 518 (596)
T PLN00044 513 WNLRVE 518 (596)
T ss_pred ehhhcc
Confidence 999999
No 38
>PRK02888 nitrous-oxide reductase; Validated
Probab=98.64 E-value=1.3e-07 Score=68.25 Aligned_cols=62 Identities=27% Similarity=0.290 Sum_probs=47.2
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEccC
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHAH 74 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~H 74 (75)
+..|++++||+|++.++|....+..+ ||+..+. .|... -+.||++.+..|+ ++||.|||+|.
T Consensus 554 p~~i~Vk~GDeVt~~lTN~d~~~DVi---HGF~Ip~----~nI~~----dv~PG~t~svtF~adkPGvy~~~Ct 616 (635)
T PRK02888 554 LREFTVKQGDEVTVIVTNLDKVEDLT---HGFAIPN----YGVNM----EVAPQATASVTFTADKPGVYWYYCT 616 (635)
T ss_pred CceEEecCCCEEEEEEEeCCcccccc---cceeecc----cCccE----EEcCCceEEEEEEcCCCEEEEEECC
Confidence 56799999999999999963312233 7776643 22222 3789999999999 99999999995
No 39
>TIGR02657 amicyanin amicyanin. Members of this family are amicyanin, a type I blue copper protein that accepts electrons from the tryptophan tryptophylquinone (TTQ) cofactor of the methylamine dehydrogenase light chain and then transfers them to the heme group of cytochrome c-551i. Amicyanin, methylamine dehydrogenase, and cytochrome c-551i are periplasmic and form a complex. This system has been studied primarily in Paracoccus denitrificans and Methylobacterium extorquens. Related type I blue copper proteins include plastocyanin, pseudoazurin, halocyanin, etc.
Probab=98.59 E-value=5.9e-07 Score=49.58 Aligned_cols=62 Identities=18% Similarity=0.208 Sum_probs=40.2
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEcCCCeeeEEccC
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFTANAGTHFWHAH 74 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~~~~Gt~~YH~H 74 (75)
+..|+++.||+|+ +.|... .+|++++..-.... .+ .....+.||+++++.| +.+|+|-|+|=
T Consensus 10 P~~i~v~~GdtVt--~~N~d~-~~Hnv~~~~g~~~~---~~----~~~~~~~~g~~~~~tf-~~~G~y~y~C~ 71 (83)
T TIGR02657 10 TPELHVKVGDTVT--WINREA-MPHNVHFVAGVLGE---AA----LKGPMMKKEQAYSLTF-TEAGTYDYHCT 71 (83)
T ss_pred CCEEEECCCCEEE--EEECCC-CCccEEecCCCCcc---cc----ccccccCCCCEEEEEC-CCCEEEEEEcC
Confidence 5679999999975 578866 68888765421110 11 0111256777777655 56899999993
No 40
>TIGR02376 Cu_nitrite_red nitrite reductase, copper-containing. This family consists of copper-type nitrite reductase. It reduces nitrite to nitric oxide, the first step in denitrification.
Probab=98.54 E-value=1.9e-07 Score=62.66 Aligned_cols=71 Identities=18% Similarity=0.133 Sum_probs=56.6
Q ss_pred cEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCc------ccccccCCCCEEEEEEc-CCCeeeEEccCC
Q psy88 4 PKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPF------VTQCPITQGNTFRYQFT-ANAGTHFWHAHT 75 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~------~~~~~i~pG~~~~y~~~-~~~Gt~~YH~H~ 75 (75)
.+.++.|+.+++++.|........+|.+|...... ..||.+. .....|.||+++...++ +++|.|+.+||.
T Consensus 203 ~~~v~~G~~~RlRiiNa~~~~~~~~~~~g~~~~~v-~~DG~~~~~~~~~~~~~~i~PG~R~dv~v~~~~pG~y~~~~~~ 280 (311)
T TIGR02376 203 DNALTAGVGERVLFVHSQPNRDSRPHLIGGHGDYV-WVTGKFANPPNRDVETWFIPGGSAAAALYTFEQPGVYAYVDHN 280 (311)
T ss_pred CcccccCCcEEEEEEcCCCCCCCCCeEecCCceEE-EECCcccCCCCCCcceEEECCCceEEEEEEeCCCeEEEEECcH
Confidence 46799999999999998764668899999776533 3577532 23456899999999999 889999999983
No 41
>PRK02710 plastocyanin; Provisional
Probab=98.43 E-value=2.7e-06 Score=49.91 Aligned_cols=59 Identities=17% Similarity=0.220 Sum_probs=41.4
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEcCCCeeeEEcc
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFTANAGTHFWHA 73 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~~~~Gt~~YH~ 73 (75)
+..|+++.||+|+ +.|... .+|++.+.|.. +.. .+...+.||+++++.|.. +|+|-|+|
T Consensus 46 P~~i~v~~Gd~V~--~~N~~~-~~H~v~~~~~~--------~~~-~~~~~~~pg~t~~~tF~~-~G~y~y~C 104 (119)
T PRK02710 46 PSTLTIKAGDTVK--WVNNKL-APHNAVFDGAK--------ELS-HKDLAFAPGESWEETFSE-AGTYTYYC 104 (119)
T ss_pred CCEEEEcCCCEEE--EEECCC-CCceEEecCCc--------ccc-ccccccCCCCEEEEEecC-CEEEEEEc
Confidence 4679999999855 568766 68887765421 100 011237899999988886 89999999
No 42
>PF00394 Cu-oxidase: Multicopper oxidase; InterPro: IPR001117 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 1 (blue) domains. These domains are also present in proteins that have lost the ability to bind copper.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1RZP_A 2AVF_D 1NIA_A 1KCB_A 2NRD_A 1NIB_A 2BW4_A 1RZQ_C 2BWD_A 2BWI_A ....
Probab=98.39 E-value=8.4e-07 Score=54.10 Aligned_cols=71 Identities=18% Similarity=0.191 Sum_probs=55.7
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcc----cccccCCCCEEEEEEc-CC-CeeeEEcc
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFV----TQCPITQGNTFRYQFT-AN-AGTHFWHA 73 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~----~~~~i~pG~~~~y~~~-~~-~Gt~~YH~ 73 (75)
..+|.+++|++++++|.|........++..|..+... ..||.+.. ....|.||++++..++ ++ +|.||..+
T Consensus 59 ~~~~~v~~g~~~rlRliNa~~~~~~~~~i~gh~~~Vi-a~DG~~v~p~~~~~l~l~~G~R~dvlv~~~~~~g~y~i~~ 135 (159)
T PF00394_consen 59 PPVIKVKPGERYRLRLINAGASTSFNFSIDGHPMTVI-AADGVPVEPYKVDTLVLAPGQRYDVLVTADQPPGNYWIRA 135 (159)
T ss_dssp SGEEEEETTTEEEEEEEEESSS-BEEEEETTBCEEEE-EETTEEEEEEEESBEEE-TTEEEEEEEEECSCSSEEEEEE
T ss_pred cceEEEcCCcEEEEEEEeccCCeeEEEEeeccceeEe-eeccccccccccceEEeeCCeEEEEEEEeCCCCCeEEEEE
Confidence 4689999999999999999875567889999866543 47886532 3455899999999999 65 99999876
No 43
>PRK10883 FtsI repressor; Provisional
Probab=98.35 E-value=1.1e-06 Score=61.77 Aligned_cols=66 Identities=11% Similarity=0.102 Sum_probs=46.6
Q ss_pred cEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCc-------ccccccCCCCEEEEEEc-CCCe----eeEE
Q psy88 4 PKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPF-------VTQCPITQGNTFRYQFT-ANAG----THFW 71 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~-------~~~~~i~pG~~~~y~~~-~~~G----t~~Y 71 (75)
.++++.|++.++++.|. .+|.||.||..+.... .||.+. -.+..| + ++.+..++ +..+ .|+|
T Consensus 376 ~~~~~~g~~e~W~~~n~---~~HP~HlHg~~FqVl~-~~G~~~~~~~~gwkDTV~v-~-~~v~i~~~f~~~~~~~~~~m~ 449 (471)
T PRK10883 376 DVTAQQGTWERWTVRAD---MPQAFHIEGVMFLIRN-VNGAMPFPEDRGWKDTVWV-D-GQVELLVYFGQPSWAHFPFLF 449 (471)
T ss_pred eeecCCCCEEEEEEECC---CCcCEeECCccEEEEE-ecCCCCCccccCcCcEEEc-C-CeEEEEEEecCCCCCCCcEEe
Confidence 35799999999999996 4799999999877542 455421 123334 3 45777777 5444 7999
Q ss_pred ccCC
Q psy88 72 HAHT 75 (75)
Q Consensus 72 H~H~ 75 (75)
|||.
T Consensus 450 HCHi 453 (471)
T PRK10883 450 YSQT 453 (471)
T ss_pred eccc
Confidence 9994
No 44
>PF00127 Copper-bind: Copper binding proteins, plastocyanin/azurin family; InterPro: IPR000923 Blue (type 1) copper proteins are small proteins which bind a single copper atom and which are characterised by an intense electronic absorption band near 600 nm [, ]. The most well known members of this class of proteins are the plant chloroplastic plastocyanins, which exchange electrons with cytochrome c6, and the distantly related bacterial azurins, which exchange electrons with cytochrome c551. This family of proteins also includes amicyanin from bacteria such as Methylobacterium extorquens or Paracoccus versutus (Thiobacillus versutus) that can grow on methylamine; auracyanins A and B from Chloroflexus aurantiacus []; blue copper protein from Alcaligenes faecalis; cupredoxin (CPC) from Cucumis sativus (Cucumber) peelings []; cusacyanin (basic blue protein; plantacyanin, CBP) from cucumber; halocyanin from Natronomonas pharaonis (Natronobacterium pharaonis) [], a membrane associated copper-binding protein; pseudoazurin from Pseudomonas; rusticyanin from Thiobacillus ferrooxidans []; stellacyanin from Rhus vernicifera (Japanese lacquer tree); umecyanin from the roots of Armoracia rusticana (Horseradish); and allergen Ra3 from ragweed. This pollen protein is evolutionary related to the above proteins, but seems to have lost the ability to bind copper. Although there is an appreciable amount of divergence in the sequences of all these proteins, the copper ligand sites are conserved.; GO: 0005507 copper ion binding, 0009055 electron carrier activity; PDB: 1UAT_A 1CUO_A 1PLC_A 4PCY_A 3PCY_A 1PND_A 1PNC_A 1JXG_A 6PCY_A 1TKW_A ....
Probab=98.30 E-value=1.8e-06 Score=48.98 Aligned_cols=68 Identities=21% Similarity=0.179 Sum_probs=40.2
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCC-CCCcccccccCCCCEEEEEEcCCCeeeEEcc
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSD-GVPFVTQCPITQGNTFRYQFTANAGTHFWHA 73 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~D-G~~~~~~~~i~pG~~~~y~~~~~~Gt~~YH~ 73 (75)
+..|++++||+|+ +.|... .+|++.+=--..+.....+ ..+......+.||+++++.|. .+|+|.|+|
T Consensus 16 P~~i~V~~G~tV~--~~n~~~-~~Hnv~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~tF~-~~G~y~y~C 84 (99)
T PF00127_consen 16 PSEITVKAGDTVT--FVNNDS-MPHNVVFVADGMPAGADSDYVPPGDSSPLLAPGETYSVTFT-KPGTYEYYC 84 (99)
T ss_dssp SSEEEEETTEEEE--EEEESS-SSBEEEEETTSSHTTGGHCHHSTTCEEEEBSTTEEEEEEEE-SSEEEEEEE
T ss_pred CCEEEECCCCEEE--EEECCC-CCceEEEecccccccccccccCccccceecCCCCEEEEEeC-CCeEEEEEc
Confidence 4679999999865 555444 6777765221000000000 000001234779999888887 889999999
No 45
>KOG1263|consensus
Probab=98.14 E-value=6.4e-06 Score=59.25 Aligned_cols=72 Identities=17% Similarity=0.186 Sum_probs=52.9
Q ss_pred cEEEecCCEEEEEEEeCCCC--CCceEEeCCccccCCC-----CCC---C--------CCcccccccCCCCEEEEEEc-C
Q psy88 4 PKNVCEGDRVVVDVRNSMDG--LENTIHWHGIHQRGTQ-----YSD---G--------VPFVTQCPITQGNTFRYQFT-A 64 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~~--~~~~iH~HG~~~~~~~-----~~D---G--------~~~~~~~~i~pG~~~~y~~~-~ 64 (75)
.++++-++.|+|.+.|.... ..+++|+||..+.... |.. - .+...+.-|+||.-...+|. +
T Consensus 431 v~~~~~~~~veIVlqN~~~~~~~~hp~HLHG~~F~Vvg~g~G~~~~~~d~~~~yNl~dp~~R~Tv~V~pggw~aIrf~ad 510 (563)
T KOG1263|consen 431 VMKLEFNSFVEIVLQNTSTGTQENHPNHLHGYNFYVVGYGFGNWDPAKDPRKKYNLVDPVSRDTVQVPPGGWTAIRFVAD 510 (563)
T ss_pred EEEeecCCEEEEEEeCCccccCCCCccceeceEEEEEEecccccCcCcChhhhcccCCCcccceEEeCCCCEEEEEEEcC
Confidence 36888999999999998652 3577799998754221 111 1 01112455899999999999 9
Q ss_pred CCeeeEEccCC
Q psy88 65 NAGTHFWHAHT 75 (75)
Q Consensus 65 ~~Gt~~YH~H~ 75 (75)
+||.|.+|||.
T Consensus 511 NPG~W~~HCHi 521 (563)
T KOG1263|consen 511 NPGVWLMHCHI 521 (563)
T ss_pred CCcEEEEEEec
Confidence 99999999994
No 46
>TIGR03102 halo_cynanin halocyanin domain. Halocyanins are blue (type I) copper redox proteins found in halophilic archaea such as Natronobacterium pharaonis. This model represents a domain duplicated in some halocyanins, while appearing once in others. This domain includes the characteristic copper ligand residues. This family does not include plastocyanins, and does not include certain divergent paralogs of halocyanin.
Probab=97.98 E-value=0.0001 Score=43.28 Aligned_cols=60 Identities=18% Similarity=0.212 Sum_probs=37.9
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEcCCCeeeEEcc
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFTANAGTHFWHA 73 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~~~~Gt~~YH~ 73 (75)
+..|+++.||+|+ ++|+.+..+|++..-+ ... .| .......+|+++++.| +.+|+|-|+|
T Consensus 41 P~~ltV~~GdTVt--w~~~~d~~~HnV~s~~----~~~-f~----s~~~~~~~G~t~s~Tf-~~~G~Y~Y~C 100 (115)
T TIGR03102 41 PPAIRVDPGTTVV--WEWTGEGGGHNVVSDG----DGD-LD----ESERVSEEGTTYEHTF-EEPGIYLYVC 100 (115)
T ss_pred CCEEEECCCCEEE--EEECCCCCCEEEEECC----CCC-cc----ccccccCCCCEEEEEe-cCCcEEEEEc
Confidence 4678999999977 5554332566665311 000 11 0111257899998888 5689999999
No 47
>TIGR02375 pseudoazurin pseudoazurin. Pseudoazurin, also called cupredoxin, is a small, blue periplasmic protein with a single bound copper atom. Pseudoazurin is related plastocyanins. Several examples of pseudoazurin are encoded by a neighboring gene for, or have been shown to transfer electrons to, copper-containing nitrite reductases (TIGR02376) of the same species.
Probab=97.79 E-value=0.0001 Score=43.37 Aligned_cols=58 Identities=10% Similarity=0.116 Sum_probs=33.7
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEe-CCccccCCCCCCCCCcccccccCCCCEEEEEEcCCCeeeEEcc
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHW-HGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFTANAGTHFWHA 73 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~-HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~~~~Gt~~YH~ 73 (75)
+..|+++.||+|++...|. +++..+ -+. ..+|.... ...+|+++++.| +.+|+|-|.|
T Consensus 14 P~~v~V~~GdTV~f~n~d~----~Hnv~~~~~~------~p~g~~~~---~s~~g~~~~~tF-~~~G~Y~Y~C 72 (116)
T TIGR02375 14 PAYIRAAPGDTVTFVPTDK----GHNVETIKGM------IPEGAEAF---KSKINEEYTVTV-TEEGVYGVKC 72 (116)
T ss_pred CCEEEECCCCEEEEEECCC----CeeEEEccCC------CcCCcccc---cCCCCCEEEEEe-CCCEEEEEEc
Confidence 5679999999977765543 455443 111 11332211 123455544444 6789999999
No 48
>COG3794 PetE Plastocyanin [Energy production and conversion]
Probab=97.63 E-value=0.00051 Score=41.10 Aligned_cols=60 Identities=17% Similarity=0.131 Sum_probs=36.7
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEcCCCeeeEEcc
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFTANAGTHFWHA 73 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~~~~Gt~~YH~ 73 (75)
+-.|+++.||+|+ +.|... ..|+++.=+.. ..+|... ....+|+++++.| +.+|.|-|.|
T Consensus 53 PA~v~v~pGDTVt--w~~~d~-~~Hnv~~~~~~-----~~~g~~~---~~~~~~~s~~~Tf-e~~G~Y~Y~C 112 (128)
T COG3794 53 PAEVTVKPGDTVT--WVNTDS-VGHNVTAVGGM-----DPEGSGT---LKAGINESFTHTF-ETPGEYTYYC 112 (128)
T ss_pred CcEEEECCCCEEE--EEECCC-CCceEEEeCCC-----Ccccccc---cccCCCcceEEEe-cccceEEEEe
Confidence 4578999999965 567765 57777653332 1122221 1233445555555 4589999999
No 49
>PF00116 COX2: Cytochrome C oxidase subunit II, periplasmic domain This family corresponds to chains b and o.; InterPro: IPR002429 Cytochrome c oxidase (1.9.3.1 from EC) [, ] is an oligomeric enzymatic complex which is a component of the respiratory chain and is involved in the transfer of electrons from cytochrome c to oxygen. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. The number of polypeptides in the complex ranges from 3-4 (prokaryotes), up to 13(mammals). Subunit 2 (CO II) transfers the electrons from cytochrome c to the catalytic subunit 1. It contains two adjacent transmembrane regions in its N terminus and the major part of the protein is exposed to the periplasmic or to the mitochondrial intermembrane space, respectively. CO II provides the substrate-binding site and contains a copper centre called Cu(A), probably the primary acceptor in cytochrome c oxidase. An exception is the corresponding subunit of the cbb3-type oxidase which lacks the copper A redox-centre. Several bacterial CO II have a C-terminal extension that contains a covalently bound haem c.; GO: 0004129 cytochrome-c oxidase activity, 0005507 copper ion binding, 0016020 membrane; PDB: 3OMN_D 3OMA_B 3OMI_D 3OM3_B 3EHB_B 1AR1_B 1QLE_B 3HB3_B 2IWK_B 2IWF_A ....
Probab=97.38 E-value=0.0016 Score=38.34 Aligned_cols=58 Identities=17% Similarity=0.173 Sum_probs=42.6
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEccC
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHAH 74 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~H 74 (75)
...|++..|+.|++.+++.. .- ||+..+.. |. ...+.||+.....|. +.+|+|...|-
T Consensus 45 ~~~l~lp~g~~v~~~ltS~D--Vi-----Hsf~ip~~----~~----k~d~~PG~~~~~~~~~~~~G~y~~~C~ 103 (120)
T PF00116_consen 45 DNELVLPAGQPVRFHLTSED--VI-----HSFWIPEL----GI----KMDAIPGRTNSVTFTPDKPGTYYGQCA 103 (120)
T ss_dssp SSEEEEETTSEEEEEEEESS--S------EEEEETTC----TE----EEEEBTTCEEEEEEEESSSEEEEEEE-
T ss_pred cceecccccceEeEEEEcCC--cc-----cccccccc----Cc----ccccccccceeeeeeeccCCcEEEcCc
Confidence 35789999999999999964 23 45544321 11 123679999999999 99999999984
No 50
>TIGR03094 sulfo_cyanin sulfocyanin. Members of this family are blue-copper redox proteins designated sulfocyanin, from the archaeal genera Sulfolobus, Ferroplasma, and Picrophilus. The most closely related proteins characterized as functionally different are the rustacyanins.
Probab=97.16 E-value=0.0055 Score=38.78 Aligned_cols=69 Identities=16% Similarity=0.113 Sum_probs=48.3
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEeCCccccC------CCCCCCCCcc----c-----ccccCCCCEEEEEEc-CC
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRG------TQYSDGVPFV----T-----QCPITQGNTFRYQFT-AN 65 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~------~~~~DG~~~~----~-----~~~i~pG~~~~y~~~-~~ 65 (75)
.++|.+-.|=+|.|+|.|... .+|++-. +.... ....||.... + ..-+.+|++..-.|. -+
T Consensus 84 ~mtIyiPaGw~V~V~f~N~e~-~pHnl~i--v~n~t~~P~~~~~s~dgkil~~vG~~~s~~~~NGi~~Gqs~sg~~~~~~ 160 (195)
T TIGR03094 84 AMTIYLPAGWNVYVTFTNYES-LPHNLKL--LPNSTQTPRGPIWAHTGKIINSTGATTSIYYGNGISSGHSRSGWWNDTS 160 (195)
T ss_pred ceEEEEeCCCEEEEEEEcCCC-CCccEEE--ecCCCCCCCccccccCceeEeecccccCccccccccccceeEEEeccCC
Confidence 578999999999999999987 7877654 22111 1234553211 1 133568889777777 89
Q ss_pred CeeeEEcc
Q psy88 66 AGTHFWHA 73 (75)
Q Consensus 66 ~Gt~~YH~ 73 (75)
+|+|||=|
T Consensus 161 ~G~YwlvC 168 (195)
T TIGR03094 161 AGKYWLVC 168 (195)
T ss_pred CeeEEEEc
Confidence 99999988
No 51
>PF06525 SoxE: Sulfocyanin (SoxE); InterPro: IPR010532 Members of this family are blue-copper redox proteins designated sulfocyanin, from the archaeal genera Sulfolobus, Ferroplasma, and Picrophilus. The most closely related proteins characterised as functionally different are the rusticyanins.
Probab=97.15 E-value=0.0059 Score=38.93 Aligned_cols=71 Identities=18% Similarity=0.122 Sum_probs=47.9
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEeC--Ccccc--CCCCCCCCCc----c-----cccccCCCCEEEEEEc-CCCe
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHWH--GIHQR--GTQYSDGVPF----V-----TQCPITQGNTFRYQFT-ANAG 67 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~H--G~~~~--~~~~~DG~~~----~-----~~~~i~pG~~~~y~~~-~~~G 67 (75)
.++|.+-.|-+|.|+|+|... .+|++=.= +...+ .....||... . ....|.+|++..-.|. -++|
T Consensus 85 ~m~i~VPAGw~V~i~f~N~~~-l~Hnl~iv~~~~~~p~~~~i~~DgkIl~~~G~s~~~~~~~GI~~G~s~~~~~~~l~aG 163 (196)
T PF06525_consen 85 QMTIYVPAGWNVQITFTNQES-LPHNLVIVQNDTPTPNNPPISSDGKILLYVGASPGNYTSNGISSGQSASGVYNDLPAG 163 (196)
T ss_pred cEEEEEcCCCEEEEEEEcCCC-CCeeEEEEeCCCCCCCccccCCCCceeeeccCCCCccccCCccCCceeeEEEccCCCc
Confidence 478999999999999999876 67654321 11111 1223565221 0 1234778999988887 8899
Q ss_pred eeEEcc
Q psy88 68 THFWHA 73 (75)
Q Consensus 68 t~~YH~ 73 (75)
.||+=|
T Consensus 164 ~YwlvC 169 (196)
T PF06525_consen 164 YYWLVC 169 (196)
T ss_pred eEEEEc
Confidence 999988
No 52
>COG4263 NosZ Nitrous oxide reductase [Energy production and conversion]
Probab=96.70 E-value=0.0034 Score=44.87 Aligned_cols=60 Identities=23% Similarity=0.306 Sum_probs=39.0
Q ss_pred ccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEcc
Q psy88 3 YPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHA 73 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~ 73 (75)
.++.+++||+|++.+.|-.. ..-.+ ||...+ +-|+.. .+.|-++-.|.|. +.+|.+||.|
T Consensus 558 ~ef~Vkq~DEVt~l~tnld~-Ved~t--hgfv~p----~~~v~~----~v~pq~tasvtf~a~kpgv~w~yc 618 (637)
T COG4263 558 TEFKVKQGDEVTVLTTNLDE-VEDLT--HGFVIP----NYGVNM----EVKPQRTASVTFYADKPGVAWYYC 618 (637)
T ss_pred EEEEEecCcEEEEEecccce-ecccc--ceeeec----cCceEE----EEccCCceEEEEEccCCeeeehhh
Confidence 45667777777777777644 22222 454433 223222 2778888899999 9999999987
No 53
>TIGR02695 azurin azurin. Azurin is a blue copper-binding protein in the plastocyanin/azurin family (see Pfam model pfam00127). It serves as a redox partner to enzymes such as nitrite reductase or arsenite oxidase. The most closely related copper-binding proteins to this family are auracyanins, as in Chloroflexus aurantiacus, which have similar redox activities.
Probab=96.69 E-value=0.015 Score=34.63 Aligned_cols=70 Identities=14% Similarity=0.151 Sum_probs=41.8
Q ss_pred cEEEec-CCEEEEEEEeCCCCCCceEEeCCccccC--------------------CCCCCCCCcccccccCCCCEEEEEE
Q psy88 4 PKNVCE-GDRVVVDVRNSMDGLENTIHWHGIHQRG--------------------TQYSDGVPFVTQCPITQGNTFRYQF 62 (75)
Q Consensus 4 ~i~~~~-Gd~v~i~~~N~~~~~~~~iH~HG~~~~~--------------------~~~~DG~~~~~~~~i~pG~~~~y~~ 62 (75)
.|.|+. +.+|+|+|+|... .|...--|-+.... .+..|-.-...+..|.|||+.+..|
T Consensus 17 ~i~V~a~~k~vtv~l~h~G~-lpk~~MgHN~Vl~k~~d~~~v~~~g~~ag~~~~Yvp~~d~~ViAhTkliggGes~svtF 95 (125)
T TIGR02695 17 SISVPKSCKEFTVNLKHTGK-LPKAVMGHNWVLAKSADMQAVATDGMSAGADNNYVKPGDARVIAHTKVIGGGEKTSVTF 95 (125)
T ss_pred EEEEcCCCcEEEEEEecCCc-CchhccCccEEEeccccHHHHHHHHHhcccccCccCCCCcceEEEccccCCCceEEEEE
Confidence 678887 5899999999854 44322223211110 0101100011244588999999999
Q ss_pred c-C--CCee-eEEccC
Q psy88 63 T-A--NAGT-HFWHAH 74 (75)
Q Consensus 63 ~-~--~~Gt-~~YH~H 74 (75)
. . .+|. |-|-|-
T Consensus 96 ~~~~l~~g~~Y~f~CS 111 (125)
T TIGR02695 96 DVSKLSAGEDYTFFCS 111 (125)
T ss_pred ECCCCCCCCcceEEEc
Confidence 8 4 6885 999883
No 54
>TIGR02866 CoxB cytochrome c oxidase, subunit II. Cytochrome c oxidase is the terminal electron acceptor of mitochondria (and one of several possible acceptors in prokaryotes) in the electron transport chain of aerobic respiration. The enzyme couples the oxidation of reduced cytochrome c with the reduction of molecular oxygen to water. This process results in the pumping of four protons across the membrane which are used in the proton gradient powered synthesis of ATP. The oxidase contains two heme a cofactors and three copper atoms as well as other bound ions.
Probab=95.42 E-value=0.12 Score=32.65 Aligned_cols=57 Identities=16% Similarity=0.081 Sum_probs=42.3
Q ss_pred ccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEccC
Q psy88 3 YPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHAH 74 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~H 74 (75)
..|.+..|+.|++.+++..- - ||+..+.. |+ +..+.||..-+..|. +++|+|...|-
T Consensus 117 ~~l~vp~g~~v~~~~ts~DV--~-----Hsf~ip~~----~~----k~da~PG~~~~~~~~~~~~G~y~~~c~ 174 (201)
T TIGR02866 117 NELVVPAGTPVRLQVTSKDV--I-----HSFWVPEL----GG----KIDAIPGQYNALWFNADEPGVYYGYCA 174 (201)
T ss_pred CEEEEEcCCEEEEEEEeCch--h-----hccccccc----Cc----eEEecCCcEEEEEEEeCCCEEEEEEeh
Confidence 47899999999999998632 2 66655421 21 123668999999999 99999998873
No 55
>PRK13202 ureB urease subunit beta; Reviewed
Probab=95.10 E-value=0.13 Score=29.70 Aligned_cols=60 Identities=17% Similarity=0.135 Sum_probs=39.2
Q ss_pred ccEEEecC--CEEEEEEEeCCCCCCceE--EeCCccccCCCCCC-----C----CCcccccccCCCCEEEEEEc
Q psy88 3 YPKNVCEG--DRVVVDVRNSMDGLENTI--HWHGIHQRGTQYSD-----G----VPFVTQCPITQGNTFRYQFT 63 (75)
Q Consensus 3 ~~i~~~~G--d~v~i~~~N~~~~~~~~i--H~HG~~~~~~~~~D-----G----~~~~~~~~i~pG~~~~y~~~ 63 (75)
-.|++++| ++++|.++|..+ +|..+ |+|=+........| | .|.-+...+.||++++.++.
T Consensus 11 ~~I~ln~grr~~~~l~V~NtGD-RPIQVGSHyHF~E~N~aL~FDR~~A~G~RLdIpaGTavRFEPG~~k~V~LV 83 (104)
T PRK13202 11 GDIEMNAAALSRLQMRIINAGD-RPVQVGSHVHLPQANRALSFDRATAHGYRLDIPAATAVRFEPGIPQIVGLV 83 (104)
T ss_pred CCEEeCCCCCceEEEEEEeCCC-CceEEccccchhhcCcceeecHhHhcCcccccCCCCeEEECCCCeEEEEEE
Confidence 46899999 589999999999 77655 55533322111111 1 22223455889999999887
No 56
>PRK13203 ureB urease subunit beta; Reviewed
Probab=94.33 E-value=0.28 Score=28.32 Aligned_cols=60 Identities=22% Similarity=0.265 Sum_probs=39.1
Q ss_pred ccEEEecC-CEEEEEEEeCCCCCCceE--EeCCccccCCCCCC-----C----CCcccccccCCCCEEEEEEc
Q psy88 3 YPKNVCEG-DRVVVDVRNSMDGLENTI--HWHGIHQRGTQYSD-----G----VPFVTQCPITQGNTFRYQFT 63 (75)
Q Consensus 3 ~~i~~~~G-d~v~i~~~N~~~~~~~~i--H~HG~~~~~~~~~D-----G----~~~~~~~~i~pG~~~~y~~~ 63 (75)
..|++++| ++++|.++|..+ +|..+ |+|=+........| | .|.-+...+.||++++.++.
T Consensus 11 ~~I~ln~gr~~~~l~V~NtGD-RPIQVGSH~HF~E~N~aL~FDR~~A~G~RLdIpaGTavRFEPG~~k~V~LV 82 (102)
T PRK13203 11 GEIELNAGRETVTLTVANTGD-RPIQVGSHYHFFEVNPALSFDREAARGMRLNIPAGTAVRFEPGQTREVELV 82 (102)
T ss_pred CCEEeCCCCCEEEEEEEeCCC-CceEEccccchhhcCcchhccHhhhcCcccccCCCCeEeECCCCeEEEEEE
Confidence 46788888 889999999999 78655 55543322111111 1 22223455889999999887
No 57
>TIGR00192 urease_beta urease, beta subunit. In a number of species, including B.subtilis, Synechocystis, and Haemophilus influenzae, urease subunits beta and gamma are encoded as separate polypeptides. In Helicobacter pylori UreA and in the fission yeast Schizosaccharomyces pombe, beta subunit-like sequence follows gamma subunit-like sequence in a single chain; the fission yeast protein contains additional C-terminal regions.
Probab=94.30 E-value=0.28 Score=28.21 Aligned_cols=60 Identities=23% Similarity=0.277 Sum_probs=38.9
Q ss_pred ccEEEecC-CEEEEEEEeCCCCCCceE--EeCCccccCCCCCC-----C----CCcccccccCCCCEEEEEEc
Q psy88 3 YPKNVCEG-DRVVVDVRNSMDGLENTI--HWHGIHQRGTQYSD-----G----VPFVTQCPITQGNTFRYQFT 63 (75)
Q Consensus 3 ~~i~~~~G-d~v~i~~~N~~~~~~~~i--H~HG~~~~~~~~~D-----G----~~~~~~~~i~pG~~~~y~~~ 63 (75)
-.|+++.| ++++|.++|..+ +|..+ |+|=+........| | .|.-+...+.||++++.++.
T Consensus 11 ~~I~ln~gr~~~~l~V~NtGD-RPIQVGSHyHF~E~N~aL~FDR~~A~G~RLdIpaGTavRFEPG~~k~V~LV 82 (101)
T TIGR00192 11 GDITINEGRKTVSVKVKNTGD-RPIQVGSHFHFFEVNRALDFDRELAFGMRLDIPSGTAVRFEPGEEKSVELV 82 (101)
T ss_pred CCEEeCCCCcEEEEEEEeCCC-cceEEccccchhhcCcceeecHhhhcCcccccCCCCeEeECCCCeEEEEEE
Confidence 35788888 889999999999 77655 55543322111111 1 22223455899999999887
No 58
>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=93.89 E-value=0.34 Score=26.65 Aligned_cols=32 Identities=25% Similarity=0.480 Sum_probs=17.7
Q ss_pred CCCCCCc---ccccccCCCCEEEEEEc---CC--CeeeEE
Q psy88 40 YSDGVPF---VTQCPITQGNTFRYQFT---AN--AGTHFW 71 (75)
Q Consensus 40 ~~DG~~~---~~~~~i~pG~~~~y~~~---~~--~Gt~~Y 71 (75)
|++|... +....|+||++.+|++. .. +|+|..
T Consensus 41 wS~~~~FtQal~~~~l~pGe~~~~~~~~~~~~~~~G~Y~~ 80 (82)
T PF12690_consen 41 WSDGKMFTQALQEETLEPGESLTYEETWDLKDLSPGEYTL 80 (82)
T ss_dssp TTTT-------EEEEE-TT-EEEEEEEESS----SEEEEE
T ss_pred ecCCchhhheeeEEEECCCCEEEEEEEECCCCCCCceEEE
Confidence 4555332 23456899999999988 33 788753
No 59
>cd00407 Urease_beta Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of external and internally-generated urea as a nitrogen source. The enzyme consists of three subunits, alpha, beta and gamma, which can exist as separate proteins or can be fused on a single protein chain. The alpha-beta-gamma heterotrimer forms multimers, mainly trimers. The large alpha subunit is the catalytic domain containing an active site with a bi-nickel center complexed by a carbamylated lysine. The beta and gamma subunits play a role in subunit association to form the higher order trimers.
Probab=93.88 E-value=0.42 Score=27.52 Aligned_cols=60 Identities=20% Similarity=0.268 Sum_probs=38.6
Q ss_pred ccEEEecC-CEEEEEEEeCCCCCCceE--EeCCccccCCCCCC-----C----CCcccccccCCCCEEEEEEc
Q psy88 3 YPKNVCEG-DRVVVDVRNSMDGLENTI--HWHGIHQRGTQYSD-----G----VPFVTQCPITQGNTFRYQFT 63 (75)
Q Consensus 3 ~~i~~~~G-d~v~i~~~N~~~~~~~~i--H~HG~~~~~~~~~D-----G----~~~~~~~~i~pG~~~~y~~~ 63 (75)
-.|++++| ++++|.++|..+ +|..+ |+|=+........| | .|.-+...+.||++++.++.
T Consensus 11 ~~I~lN~gr~~~~l~V~NtGD-RpIQVGSH~HF~E~N~aL~FDR~~A~G~RLdIpaGTavRFEPG~~k~V~LV 82 (101)
T cd00407 11 GDIELNAGREAVTLKVKNTGD-RPIQVGSHYHFFEVNPALKFDREKAYGMRLDIPAGTAVRFEPGEEKEVELV 82 (101)
T ss_pred CCeEeCCCCCEEEEEEEeCCC-cceEEccccchhhcCccccccHHHcccceecccCCCeEEECCCCeEEEEEE
Confidence 35778888 789999999998 77655 55543322111111 1 22223455889999999887
No 60
>PRK10378 inactive ferrous ion transporter periplasmic protein EfeO; Provisional
Probab=93.35 E-value=0.59 Score=32.65 Aligned_cols=60 Identities=13% Similarity=0.040 Sum_probs=39.2
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCC-cccccccCCCCEEEEEEcCCCeeeEEcc
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVP-FVTQCPITQGNTFRYQFTANAGTHFWHA 73 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~-~~~~~~i~pG~~~~y~~~~~~Gt~~YH~ 73 (75)
+..+.+..|+ +++.++|... .++-+-. .+|.- ...-..|.||.+.++.++-.+|+|-|+|
T Consensus 43 p~~~tVpAG~-~~f~V~N~~~-~~~Efe~----------~~~~~vv~e~EnIaPG~s~~l~~~L~pGtY~~~C 103 (375)
T PRK10378 43 PMTLTVNAGK-TQFIIQNHSQ-KALEWEI----------LKGVMVVEERENIAPGFSQKMTANLQPGEYDMTC 103 (375)
T ss_pred cCceeeCCCC-EEEEEEeCCC-CcceEEe----------eccccccccccccCCCCceEEEEecCCceEEeec
Confidence 4567888996 8888899876 4433211 01110 0011358999998887665699999999
No 61
>PRK13201 ureB urease subunit beta; Reviewed
Probab=93.02 E-value=0.6 Score=28.17 Aligned_cols=60 Identities=17% Similarity=0.239 Sum_probs=38.8
Q ss_pred ccEEEecC-CEEEEEEEeCCCCCCceE--EeCCccccCCCCCC-----C----CCcccccccCCCCEEEEEEc
Q psy88 3 YPKNVCEG-DRVVVDVRNSMDGLENTI--HWHGIHQRGTQYSD-----G----VPFVTQCPITQGNTFRYQFT 63 (75)
Q Consensus 3 ~~i~~~~G-d~v~i~~~N~~~~~~~~i--H~HG~~~~~~~~~D-----G----~~~~~~~~i~pG~~~~y~~~ 63 (75)
-.|+++.| ++++|.++|..+ +|..+ |+|=+........| | .|.-+...+.||++++.++.
T Consensus 11 ~~I~lN~gr~~~~l~V~NtGD-RPIQVGSHyHF~EvN~aL~FDR~~A~G~RLdIPAGTAVRFEPG~~k~V~LV 82 (136)
T PRK13201 11 TEVEINNHHPETVIEVENTGD-RPIQVGSHFHFYEANAALDFEREMAYGKHLDIPAGAAVRFEPGDKKEVQLV 82 (136)
T ss_pred CCeEeCCCCCEEEEEEEeCCC-cceEeccccchhhcCccccccHhhhcCcccccCCCCeEeECCCCeEEEEEE
Confidence 35788888 889999999998 77655 55533322111111 1 22223456889999999887
No 62
>PRK13198 ureB urease subunit beta; Reviewed
Probab=93.00 E-value=0.54 Score=29.02 Aligned_cols=60 Identities=20% Similarity=0.211 Sum_probs=39.0
Q ss_pred ccEEEecC-CEEEEEEEeCCCCCCceE--EeCCccccCCCC-----CCC----CCcccccccCCCCEEEEEEc
Q psy88 3 YPKNVCEG-DRVVVDVRNSMDGLENTI--HWHGIHQRGTQY-----SDG----VPFVTQCPITQGNTFRYQFT 63 (75)
Q Consensus 3 ~~i~~~~G-d~v~i~~~N~~~~~~~~i--H~HG~~~~~~~~-----~DG----~~~~~~~~i~pG~~~~y~~~ 63 (75)
-+|.+++| ++++|.+.|..+ +|.-+ |+|=+....... .-| .|.-+...+.||++++.++.
T Consensus 39 g~I~lN~gr~~~~l~V~NtGD-RPIQVGSHyHF~EvN~aL~FDR~~A~G~RLdIPAGTAVRFEPG~~k~V~LV 110 (158)
T PRK13198 39 TPITFNENKPVTKVKVRNTGD-RPIQVGSHFHFFEVNRALEFDRAAAYGKRLNISSTTAIRFEPGDETEVPLI 110 (158)
T ss_pred CCeEeCCCCcEEEEEEEeCCC-CceEeccccchhhcCccccccHhhhcCcccccCCCCeEeeCCCCeeEEEEE
Confidence 35888888 899999999998 77655 555333221111 111 22223455889999999887
No 63
>PRK13205 ureB urease subunit beta; Reviewed
Probab=92.93 E-value=0.57 Score=28.93 Aligned_cols=60 Identities=18% Similarity=0.211 Sum_probs=38.7
Q ss_pred ccEEEecC-CEEEEEEEeCCCCCCceE--EeCCccccCCCCCC-----C----CCcccccccCCCCEEEEEEc
Q psy88 3 YPKNVCEG-DRVVVDVRNSMDGLENTI--HWHGIHQRGTQYSD-----G----VPFVTQCPITQGNTFRYQFT 63 (75)
Q Consensus 3 ~~i~~~~G-d~v~i~~~N~~~~~~~~i--H~HG~~~~~~~~~D-----G----~~~~~~~~i~pG~~~~y~~~ 63 (75)
-.|.+++| ++++|.++|..+ +|..+ |+|=+........| | .|.-+...+.||++++.++.
T Consensus 11 g~IelN~GR~~i~L~V~NtGD-RPIQVGSHyHF~EvN~AL~FDR~~A~G~RLdIPAGTAVRFEPGe~ktV~LV 82 (162)
T PRK13205 11 ESLTGNVGREAKTIEIINTGD-RPVQIGSHFHFAEVNPSISFDRSEGYGFRLDIPSGTAVRLEPGDARTVNLV 82 (162)
T ss_pred CCeEeCCCCcEEEEEEEeCCC-CceEeccccchhhcCccccccHHHhcCcccccCCCCeEeECCCCeEEEEEE
Confidence 35788888 889999999998 78665 55533222111111 1 22223455889999999887
No 64
>PRK13204 ureB urease subunit beta; Reviewed
Probab=92.88 E-value=0.56 Score=28.98 Aligned_cols=60 Identities=25% Similarity=0.329 Sum_probs=38.9
Q ss_pred ccEEEecC-CEEEEEEEeCCCCCCceE--EeCCccccCCCCCC-----C----CCcccccccCCCCEEEEEEc
Q psy88 3 YPKNVCEG-DRVVVDVRNSMDGLENTI--HWHGIHQRGTQYSD-----G----VPFVTQCPITQGNTFRYQFT 63 (75)
Q Consensus 3 ~~i~~~~G-d~v~i~~~N~~~~~~~~i--H~HG~~~~~~~~~D-----G----~~~~~~~~i~pG~~~~y~~~ 63 (75)
-.|+++.| ++++|.+.|..+ +|.-+ |+|=+........| | .|.-+...+.||++++.++.
T Consensus 34 ~~I~lN~gr~~~~l~V~NtGD-RPIQVGSHyHF~EvN~aL~FDR~~A~G~RLdIPAGTAVRFEPG~~k~V~LV 105 (159)
T PRK13204 34 DPIEINQGRPRTTLTVRNTGD-RPIQIGSHFHFFEVNRYLEFDRSKAFGLRLDIPANTAVRFEPGDEKEVTLV 105 (159)
T ss_pred CCeEeCCCCcEEEEEEEeCCC-CceEeccccchhhcCccccccHhhhcCcccccCCCCeEeECCCCeeEEEEE
Confidence 35788888 889999999998 77655 55543322111111 1 22223455889999999887
No 65
>COG4263 NosZ Nitrous oxide reductase [Energy production and conversion]
Probab=92.77 E-value=0.37 Score=34.87 Aligned_cols=60 Identities=7% Similarity=-0.020 Sum_probs=46.6
Q ss_pred ccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEcc
Q psy88 3 YPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHA 73 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~ 73 (75)
++.-+++++.+++.++|... .+.-.||+..- .|+..+. +.|......+|. +++|++||.|
T Consensus 548 ~~staps~~l~ef~Vkq~DE---Vt~l~tnld~V----ed~thgf----v~p~~~v~~~v~pq~tasvtf~a 608 (637)
T COG4263 548 MTSTAPSFGLTEFKVKQGDE---VTVLTTNLDEV----EDLTHGF----VIPNYGVNMEVKPQRTASVTFYA 608 (637)
T ss_pred EeeccCCCceEEEEEecCcE---EEEEeccccee----cccccee----eeccCceEEEEccCCceEEEEEc
Confidence 45567889999999999753 45666888643 4766654 778899999999 9999999987
No 66
>COG1622 CyoA Heme/copper-type cytochrome/quinol oxidases, subunit 2 [Energy production and conversion]
Probab=89.76 E-value=2.9 Score=27.59 Aligned_cols=57 Identities=16% Similarity=0.035 Sum_probs=41.5
Q ss_pred ccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEccC
Q psy88 3 YPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHAH 74 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~H 74 (75)
..|.+..|..|++.++-.. .- ||+..+.. |. +..+-||......++ +++|+|.-.|.
T Consensus 137 n~l~lPv~~~V~f~ltS~D--Vi-----HsF~IP~l----~~----k~d~iPG~~~~~~~~~~~~G~Y~g~Ca 194 (247)
T COG1622 137 NELVLPVGRPVRFKLTSAD--VI-----HSFWIPQL----GG----KIDAIPGMTTELWLTANKPGTYRGICA 194 (247)
T ss_pred ceEEEeCCCeEEEEEEech--hc-----eeEEecCC----Cc----eeeecCCceEEEEEecCCCeEEEEEcH
Confidence 5789999999999988763 22 55554421 11 223678988888888 99999998884
No 67
>PRK13192 bifunctional urease subunit gamma/beta; Reviewed
Probab=89.37 E-value=2.1 Score=27.69 Aligned_cols=60 Identities=22% Similarity=0.231 Sum_probs=38.5
Q ss_pred ccEEEecC-CEEEEEEEeCCCCCCceE--EeCCccccCCCCC-----CC----CCcccccccCCCCEEEEEEc
Q psy88 3 YPKNVCEG-DRVVVDVRNSMDGLENTI--HWHGIHQRGTQYS-----DG----VPFVTQCPITQGNTFRYQFT 63 (75)
Q Consensus 3 ~~i~~~~G-d~v~i~~~N~~~~~~~~i--H~HG~~~~~~~~~-----DG----~~~~~~~~i~pG~~~~y~~~ 63 (75)
-.|.+++| +++.+.++|..+ +|.-+ |+|=+.....-.. -| .|.-+...+.||++++.++.
T Consensus 120 ~~I~lN~gr~~~~l~V~NtGD-RPIQVGSHyHF~E~N~aL~FDR~~A~G~RLdIpAGTavRFEPG~~k~V~LV 191 (208)
T PRK13192 120 GEIELNAGRPAVTLDVTNTGD-RPIQVGSHFHFFEVNRALRFDRAAAYGMRLDIPAGTAVRFEPGETKEVRLV 191 (208)
T ss_pred CCeeeCCCCCEEEEEEEeCCC-CceeeccccchhhcCchhhccHHHhcCcccccCCCCeEeECCCCeeEEEEE
Confidence 35788888 889999999998 77655 5553322211111 11 22223455889999999887
No 68
>PF05938 Self-incomp_S1: Plant self-incompatibility protein S1; InterPro: IPR010264 This family consists of a series of plant proteins which are related to the Papaver rhoeas S1 self-incompatibility protein. Self-incompatibility (SI) is the single most important outbreeding device found in angiosperms and is a mechanism that regulates the acceptance or rejection of pollen. S1 is known to exhibit specific pollen-inhibitory properties [].
Probab=88.71 E-value=3 Score=23.66 Aligned_cols=52 Identities=17% Similarity=0.304 Sum_probs=31.1
Q ss_pred EEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEccC
Q psy88 14 VVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHAH 74 (75)
Q Consensus 14 ~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~H 74 (75)
.|.+.|.+. ....|..|=-.- ..| +....+.||+.+.++|. +-.|+-.|-|+
T Consensus 2 ~V~I~N~L~-~~~~L~vhC~S~----d~D----lg~~~l~~g~~~~~~F~~~~~~~t~f~C~ 54 (110)
T PF05938_consen 2 HVVIINNLG-PGKILTVHCKSK----DDD----LGWHVLKPGQSYSFSFRDNFFGTTLFWCH 54 (110)
T ss_pred EEEEEECCC-CCCeEEEEeeCC----Ccc----CCCEECCCCCEEEEEEecCcCCceeEEEE
Confidence 478899985 344443332211 122 11224899999999999 65566666664
No 69
>PF00699 Urease_beta: Urease beta subunit CAUTION: The Prosite patterns do not match this subunit of the enzyme; InterPro: IPR002019 Urease 3.5.1.5 from EC is a nickel-binding enzyme that catalyzes the hydrolysis of urea to carbon dioxide and ammonia []: Urea + H2O = CO2 + 2 NH3 Historically, it was the first enzyme to be crystallized (in 1926). It is mainly found in plant seeds and microorganisms. In plants, urease is a hexamer of identical chains. In bacteria [], it consists of either two or three different subunits (alpha IPR005847 from INTERPRO, beta, described in this entry, and gamma IPR002026 from INTERPRO). The structure of the urease complex is known []. This subunit does not appear to take part in the catalytic mechanism. This subunit is known (confusingly) as alpha in Helicobacter.; GO: 0009039 urease activity, 0016151 nickel ion binding, 0006807 nitrogen compound metabolic process; PDB: 1EJS_B 1EJW_B 1A5N_B 1A5K_B 1A5M_B 1EJR_B 1EJX_B 1A5L_B 1KRB_B 1FWA_B ....
Probab=88.60 E-value=0.64 Score=26.74 Aligned_cols=59 Identities=20% Similarity=0.232 Sum_probs=31.4
Q ss_pred cEEEecC-CEEEEEEEeCCCCCCceEEeCCccccCCC--CCC-----C----CCcccccccCCCCEEEEEEc
Q psy88 4 PKNVCEG-DRVVVDVRNSMDGLENTIHWHGIHQRGTQ--YSD-----G----VPFVTQCPITQGNTFRYQFT 63 (75)
Q Consensus 4 ~i~~~~G-d~v~i~~~N~~~~~~~~iH~HG~~~~~~~--~~D-----G----~~~~~~~~i~pG~~~~y~~~ 63 (75)
.|.+++| ++++|.+.|..| +|..+=.|=.++..++ ..| | .|.-+...+.||++++.++.
T Consensus 11 ~I~lN~gr~~~~l~V~N~GD-RPIQVGSH~HF~E~N~aL~FDR~~A~G~RLdIPaGTavRFEPG~~k~V~LV 81 (100)
T PF00699_consen 11 DIELNAGRERITLEVTNTGD-RPIQVGSHYHFFEVNPALEFDREAAYGMRLDIPAGTAVRFEPGDTKEVELV 81 (100)
T ss_dssp EEETTTTSEEEEEEEEE-SS-S-EEEETTS-GGGS-TTEES-HHHHTTEEE-SSTT-EEEE-TT-EEEEEEE
T ss_pred cEEecCCCcEEEEEEEeCCC-cceEEccccCHHHHhHHhhhhHHHhCCcccCcCCCCeEEECCCCcEEEEEE
Confidence 4666666 578999999999 8876633332222211 111 1 12223455889999999887
No 70
>PF10989 DUF2808: Protein of unknown function (DUF2808); InterPro: IPR021256 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=87.56 E-value=0.89 Score=27.43 Aligned_cols=25 Identities=20% Similarity=0.387 Sum_probs=20.9
Q ss_pred ccccCCCCEEEEEEc-----CCCeeeEEcc
Q psy88 49 QCPITQGNTFRYQFT-----ANAGTHFWHA 73 (75)
Q Consensus 49 ~~~i~pG~~~~y~~~-----~~~Gt~~YH~ 73 (75)
..||+||.+.+..+. ...|+|.|.|
T Consensus 96 ~~PV~pG~tv~V~l~~v~NP~~~G~Y~f~v 125 (146)
T PF10989_consen 96 DEPVPPGTTVTVVLSPVRNPRSGGTYQFNV 125 (146)
T ss_pred CCCCCCCCEEEEEEEeeeCCCCCCeEEEEE
Confidence 568999999999995 3469999876
No 71
>PRK13986 urease subunit alpha; Provisional
Probab=86.40 E-value=3.6 Score=26.90 Aligned_cols=59 Identities=19% Similarity=0.169 Sum_probs=38.0
Q ss_pred cEEEecC-CEEEEEEEeCCCCCCceE--EeCCccccCCCCC-----CC----CCcccccccCCCCEEEEEEc
Q psy88 4 PKNVCEG-DRVVVDVRNSMDGLENTI--HWHGIHQRGTQYS-----DG----VPFVTQCPITQGNTFRYQFT 63 (75)
Q Consensus 4 ~i~~~~G-d~v~i~~~N~~~~~~~~i--H~HG~~~~~~~~~-----DG----~~~~~~~~i~pG~~~~y~~~ 63 (75)
.|.+++| +++++.++|..+ +|.-+ |+|=+.....-.. -| .|.-+...+.||++++.++.
T Consensus 117 ~I~lN~gr~~~~l~V~NtGD-RPIQVGSHyHF~E~N~aL~FDR~~A~G~RLdIpAGTavRFEPG~~k~V~LV 187 (225)
T PRK13986 117 DITINAGKKAVSVKVKNVGD-RPVQVGSHFHFFEVNRCLEFDREKAFGKRLDIASGTAVRFEPGEEKSVELI 187 (225)
T ss_pred CeecCCCCcEEEEEEEeCCC-CceeeccccchhhcCchhhccHHHhcCcccccCCCCeEeECCCCeeEEEEE
Confidence 5788888 889999999998 77655 5553332211111 11 22223455889999999887
No 72
>COG4454 Uncharacterized copper-binding protein [Inorganic ion transport and metabolism]
Probab=85.61 E-value=5.8 Score=24.65 Aligned_cols=67 Identities=13% Similarity=0.107 Sum_probs=42.7
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEeCCccccC-----------CCCCCCCCcccccccCCCCEEEEEEc-CCCeee
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRG-----------TQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTH 69 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~-----------~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~ 69 (75)
+-.+.++.|++++..+.|... - .|=-.+..+. .+..++-. .....+.||++-...|. ..+|.|
T Consensus 62 p~~~~v~aG~tv~~v~~n~~e-l---~hef~~~~~~~~~~~~~~~~~~~Dme~d~-~~~v~L~PG~s~elvv~ft~~g~y 136 (158)
T COG4454 62 PSSFEVKAGETVRFVLKNEGE-L---KHEFTMDAPDKNLEHVTHMILADDMEHDD-PNTVTLAPGKSGELVVVFTGAGKY 136 (158)
T ss_pred CCcccccCCcEEeeeecCccc-c---eEEEeccCccccchhHHHhhhCCccccCC-cceeEeCCCCcEEEEEEecCCccE
Confidence 456789999999999999764 1 1211111110 01122211 12345899999999999 889999
Q ss_pred EEcc
Q psy88 70 FWHA 73 (75)
Q Consensus 70 ~YH~ 73 (75)
-+-|
T Consensus 137 e~~C 140 (158)
T COG4454 137 EFAC 140 (158)
T ss_pred EEEe
Confidence 8877
No 73
>COG0832 UreB Urea amidohydrolase (urease) beta subunit [Amino acid transport and metabolism]
Probab=85.13 E-value=5.3 Score=23.08 Aligned_cols=59 Identities=20% Similarity=0.288 Sum_probs=35.4
Q ss_pred cEEEecC-CEEEEEEEeCCCCCCceE--EeCCccccCCCCCC-----C----CCcccccccCCCCEEEEEEc
Q psy88 4 PKNVCEG-DRVVVDVRNSMDGLENTI--HWHGIHQRGTQYSD-----G----VPFVTQCPITQGNTFRYQFT 63 (75)
Q Consensus 4 ~i~~~~G-d~v~i~~~N~~~~~~~~i--H~HG~~~~~~~~~D-----G----~~~~~~~~i~pG~~~~y~~~ 63 (75)
.|++++| .++.|.+.|..+ +|.-+ |+|=.........| | .|.-+.....||+.++.++.
T Consensus 12 ~IelN~gr~~~~i~V~NtGD-RPIQVGSHfHF~EvN~aL~FDR~~a~G~RLdIpagTAVRFEPG~~k~V~LV 82 (106)
T COG0832 12 DIELNAGRPTVTIEVANTGD-RPIQVGSHFHFFEVNRALSFDREKAYGMRLDIPAGTAVRFEPGDEKEVELV 82 (106)
T ss_pred cEEEeCCCcceEEEEeecCC-CceEeecceeehhhCcceeechhhhcceEecccCCceEeeCCCCccEEEEE
Confidence 4677777 467889999998 77654 55533322111111 1 12223455789999988876
No 74
>TIGR03079 CH4_NH3mon_ox_B methane monooxygenase/ammonia monooxygenase, subunit B. Both ammonia oxidizers such as Nitrosomonas europaea and methanotrophs (obligate methane oxidizers) such as Methylococcus capsulatus each can grow only on their own characteristic substrate. However, both groups have the ability to oxidize both substrates, and so the relevant enzymes must be named here according to their ability to oxidze both. The protein family represented here reflects subunit B of both the particulate methane monooxygenase of methylotrophs and the ammonia monooxygenase of nitrifying bacteria.
Probab=83.65 E-value=2.2 Score=29.93 Aligned_cols=21 Identities=24% Similarity=0.398 Sum_probs=16.0
Q ss_pred CCCcccccccCCCCEEEEEEc
Q psy88 43 GVPFVTQCPITQGNTFRYQFT 63 (75)
Q Consensus 43 G~~~~~~~~i~pG~~~~y~~~ 63 (75)
|.......||.|||+++.++.
T Consensus 331 GL~v~d~~pI~PGETr~v~v~ 351 (399)
T TIGR03079 331 GLEVDDQSAIAPGETVEVKME 351 (399)
T ss_pred cceeCCCCCcCCCcceEEEEE
Confidence 433334668999999999987
No 75
>PF04744 Monooxygenase_B: Monooxygenase subunit B protein; InterPro: IPR006833 Ammonia monooxygenase and the particulate methane monooxygenase are both integral membrane proteins, occurring in ammonia oxidisers and methanotrophs respectively, which are thought to be evolutionarily related []. These enzymes have a relatively wide substrate specificity and can catalyse the oxidation of a range of substrates including ammonia, methane, halogenated hydrocarbons and aromatic molecules []. These enzymes are composed of 3 subunits - A (IPR003393 from INTERPRO), B (IPR006833 from INTERPRO) and C (IPR006980 from INTERPRO) - and contain various metal centres, including copper. Particulate methane monooxygenase from Methylococcus capsulatus str. Bath is an ABC homotrimer, which contains mononuclear and dinuclear copper metal centres, and a third metal centre containing a metal ion whose identity in vivo is not certain[]. The soluble regions of these enzymes derive primarily from the B subunit. This subunit forms two antiparallel beta-barrel-like structures and contains the mono- and di- nuclear copper metal centres [].; PDB: 3CHX_E 3RFR_A 3RGB_A 1YEW_A.
Probab=82.51 E-value=2.2 Score=29.93 Aligned_cols=15 Identities=27% Similarity=0.432 Sum_probs=10.0
Q ss_pred ccccCCCCEEEEEEc
Q psy88 49 QCPITQGNTFRYQFT 63 (75)
Q Consensus 49 ~~~i~pG~~~~y~~~ 63 (75)
..||+|||+++.+..
T Consensus 318 ~~pI~PGETrtl~V~ 332 (381)
T PF04744_consen 318 NSPIAPGETRTLTVE 332 (381)
T ss_dssp -S-B-TT-EEEEEEE
T ss_pred CCCcCCCceEEEEEE
Confidence 558999999999987
No 76
>PF05506 DUF756: Domain of unknown function (DUF756); InterPro: IPR008475 This domain is found, normally as a tandem repeat, at the C terminus of bacterial phospholipase C proteins.; GO: 0004629 phospholipase C activity, 0016042 lipid catabolic process
Probab=82.44 E-value=6.1 Score=21.56 Aligned_cols=46 Identities=13% Similarity=0.132 Sum_probs=30.6
Q ss_pred CCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc
Q psy88 10 GDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT 63 (75)
Q Consensus 10 Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~ 63 (75)
...|.|+|.|... .+..+......+ ..+.+ .+..|.||++.+..|.
T Consensus 19 ~g~l~l~l~N~g~-~~~~~~v~~~~y-----~~~~~--~~~~v~ag~~~~~~w~ 64 (89)
T PF05506_consen 19 TGNLRLTLSNPGS-AAVTFTVYDNAY-----GGGGP--WTYTVAAGQTVSLTWP 64 (89)
T ss_pred CCEEEEEEEeCCC-CcEEEEEEeCCc-----CCCCC--EEEEECCCCEEEEEEe
Confidence 3589999999977 666665443211 12222 2345899999999997
No 77
>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=80.89 E-value=9 Score=22.45 Aligned_cols=57 Identities=16% Similarity=0.436 Sum_probs=32.1
Q ss_pred EEecCCEEEEEEEeCCC--CCCceEEeCC----cccc-CCCCCCCCCcccccccCCCCEEEEEEc
Q psy88 6 NVCEGDRVVVDVRNSMD--GLENTIHWHG----IHQR-GTQYSDGVPFVTQCPITQGNTFRYQFT 63 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~~~--~~~~~iH~HG----~~~~-~~~~~DG~~~~~~~~i~pG~~~~y~~~ 63 (75)
.+++|..+.+.+.=..+ ......-.|| +..+ ..+..||=.. ..||+.+|+.++|.+.
T Consensus 23 ~l~rG~~~~~~~~F~~~~~s~~l~~~v~a~~~gv~iP~p~~~~daC~~-l~CPl~~G~~~~y~~~ 86 (120)
T cd00918 23 VIHRGKPLTLEAKFTANQDTAKAKIKITASIDGLEIDVPGIETDGCKY-VKCPIKKGQHYDIKYT 86 (120)
T ss_pred EEECCCeEEEEEEEECCCccceEEEEEEEEECCEEcCCCCCCCCCccc-EeCCCcCCcEEEEEEe
Confidence 56788888777652111 1223333344 2222 1123455322 3799999999999885
No 78
>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=80.25 E-value=4.2 Score=21.56 Aligned_cols=20 Identities=25% Similarity=0.429 Sum_probs=13.6
Q ss_pred ccCCCCEEEEEEc-C-----CCeeeE
Q psy88 51 PITQGNTFRYQFT-A-----NAGTHF 70 (75)
Q Consensus 51 ~i~pG~~~~y~~~-~-----~~Gt~~ 70 (75)
.|+||++.+..|. . .+|+|.
T Consensus 45 ~l~pG~s~~~~~~V~vp~~a~~G~y~ 70 (78)
T PF10633_consen 45 SLPPGESVTVTFTVTVPADAAPGTYT 70 (78)
T ss_dssp -B-TTSEEEEEEEEEE-TT--SEEEE
T ss_pred cCCCCCEEEEEEEEECCCCCCCceEE
Confidence 5899999999988 2 367764
No 79
>MTH00047 COX2 cytochrome c oxidase subunit II; Provisional
Probab=79.15 E-value=14 Score=23.53 Aligned_cols=57 Identities=14% Similarity=0.061 Sum_probs=37.9
Q ss_pred ccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEccC
Q psy88 3 YPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHAH 74 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~H 74 (75)
.++++..|..+++.++-.. .- |++..+.. .+ +.-.-||......+. +++|+|.--|.
T Consensus 116 ~~l~lp~g~~v~~~ltS~D--Vi-----Hsf~vp~l---~~-----k~d~~PG~~~~~~~~~~~~G~y~g~C~ 173 (194)
T MTH00047 116 KPLRLVYGVPYHLLVTSSD--VI-----HSFSVPDL---NL-----KMDAIPGRINHLFFCPDRHGVFVGYCS 173 (194)
T ss_pred ceEEEeCCCEEEeeeecCc--cc-----cceecccc---Cc-----eeecCCCceEEEEEEcCCCEEEEEEee
Confidence 3577888999888887653 22 55544321 11 112558999888888 99999987763
No 80
>COG2967 ApaG Uncharacterized protein affecting Mg2+/Co2+ transport [Inorganic ion transport and metabolism]
Probab=78.61 E-value=3.3 Score=24.65 Aligned_cols=48 Identities=21% Similarity=0.285 Sum_probs=27.8
Q ss_pred EEEEEeCCCCCC---ceEEeCCccccCC---CCCCCCCcccccccCCCCEEEEEEc
Q psy88 14 VVDVRNSMDGLE---NTIHWHGIHQRGT---QYSDGVPFVTQCPITQGNTFRYQFT 63 (75)
Q Consensus 14 ~i~~~N~~~~~~---~~iH~HG~~~~~~---~~~DG~~~~~~~~i~pG~~~~y~~~ 63 (75)
+|++.|..+ .+ .+=||+=.+.... -.-+|+-+ .|-.+.||++|+|.--
T Consensus 33 titI~N~g~-~~vqLlsR~W~ITd~~g~v~eV~G~GVVG-eQP~l~PG~~y~YtSg 86 (126)
T COG2967 33 TVTIRNLGE-VPVQLLSRYWLITDGNGRVTEVEGEGVVG-EQPLLAPGEEYQYTSG 86 (126)
T ss_pred EEEEecCCC-ccceeeeeEEEEecCCCcEEEEEcCceec-cccccCCCCceEEcCC
Confidence 578889876 44 3447764332210 01123322 3667899999999843
No 81
>MTH00140 COX2 cytochrome c oxidase subunit II; Provisional
Probab=77.40 E-value=17 Score=23.55 Aligned_cols=56 Identities=14% Similarity=0.049 Sum_probs=39.0
Q ss_pred cEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEccC
Q psy88 4 PKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHAH 74 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~H 74 (75)
.|.+-.|..|++.+++..- - |+...+. -|.. .-+-||......+. +.+|.|+-.|.
T Consensus 141 ~l~lP~~~~v~~~~ts~DV--i-----Hsf~ip~----~~~k----~d~~Pg~~~~~~~~~~~~g~y~~~C~ 197 (228)
T MTH00140 141 RLVLPYSVDTRVLVTSADV--I-----HSWTVPS----LGVK----VDAIPGRLNQLSFEPKRPGVFYGQCS 197 (228)
T ss_pred eEEEeeCcEEEEEEEcCcc--c-----cceeccc----cCce----eECCCCcceeEEEEeCCCEEEEEECc
Confidence 5788889999999988532 2 5555442 2222 12568888888888 99999987773
No 82
>PF00386 C1q: C1q domain; InterPro: IPR001073 This entry represents the C-terminal domain of C1q. C1q is a subunit of the C1 enzyme complex that activates the serum complement system. C1q comprises 6 A, 6 B and 6 C chains. These share the same topology, each possessing a small, globular N-terminal domain, a collagen-like Gly/Pro-rich central region, and a conserved C-terminal region, the C1q domain []. The C1q protein is produced in collagen-producing cells and shows sequence and structural similarity to collagens VIII and X [, ]. This domain is also found in multimerin and EMILIN proteins.; PDB: 1O91_C 2JG8_D 2JG9_A 2WNV_A 2WNU_A 1PK6_A 4DOU_A 1C3H_C 1C28_C 2OII_A ....
Probab=77.35 E-value=3.2 Score=23.89 Aligned_cols=18 Identities=22% Similarity=0.254 Sum_probs=13.2
Q ss_pred ccEEEecCCEEEEEEEeC
Q psy88 3 YPKNVCEGDRVVVDVRNS 20 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N~ 20 (75)
..+.+++||+|.|++...
T Consensus 91 ~vl~L~~GD~V~v~~~~~ 108 (127)
T PF00386_consen 91 AVLQLNKGDTVWVRLDSG 108 (127)
T ss_dssp EEEEE-TT-EEEEEEEEE
T ss_pred EEEEeCCCCEEEEEEecC
Confidence 367899999999999853
No 83
>PLN02303 urease
Probab=74.76 E-value=10 Score=29.34 Aligned_cols=59 Identities=24% Similarity=0.268 Sum_probs=38.2
Q ss_pred cEEEecC-CEEEEEEEeCCCCCCceE--EeCCccccCCCCCC-----C----CCcccccccCCCCEEEEEEc
Q psy88 4 PKNVCEG-DRVVVDVRNSMDGLENTI--HWHGIHQRGTQYSD-----G----VPFVTQCPITQGNTFRYQFT 63 (75)
Q Consensus 4 ~i~~~~G-d~v~i~~~N~~~~~~~~i--H~HG~~~~~~~~~D-----G----~~~~~~~~i~pG~~~~y~~~ 63 (75)
.|++++| +++++.++|..+ +|..+ |+|=+........| | .|.-+...+.||++++.++.
T Consensus 142 ~i~~n~gr~~~~l~v~n~gd-rpiqvgSH~hf~e~N~aL~FdR~~a~G~rLdipaGtavRfePG~~~~V~lv 212 (837)
T PLN02303 142 SIIINAGRKAVKLKVTNTGD-RPIQVGSHYHFIETNPYLVFDRRKAYGMRLNIPAGTAVRFEPGETKTVTLV 212 (837)
T ss_pred CeeeCCCCCeEEEEEeeCCC-CceEeccccchHhcCchhhccHHHhcCccccCCCCCeEeECCCCeeEEEEE
Confidence 5778887 789999999999 78665 55533322111111 1 22223455889999999887
No 84
>PRK05461 apaG CO2+/MG2+ efflux protein ApaG; Reviewed
Probab=73.60 E-value=8.7 Score=22.88 Aligned_cols=15 Identities=27% Similarity=0.474 Sum_probs=11.2
Q ss_pred ccccCCCCEEEEEEc
Q psy88 49 QCPITQGNTFRYQFT 63 (75)
Q Consensus 49 ~~~i~pG~~~~y~~~ 63 (75)
|-.|.||++|.|.=-
T Consensus 73 qP~L~PGe~F~Y~S~ 87 (127)
T PRK05461 73 QPVLAPGESFEYTSG 87 (127)
T ss_pred CceECCCCCeEEeCC
Confidence 344789999999744
No 85
>PF09394 Inhibitor_I42: Chagasin family peptidase inhibitor I42; InterPro: IPR018990 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. Chagasin reversible inhibitor of papain-like cysteine proteases []. Chagasin has a beta-barrel structure, which is a unique variant of the immunoglobulin fold with homology to human CD8alpha [, ].; PDB: 2NQD_A 2NNR_A 2H7W_B 3E1Z_A 3CBK_B 3CBJ_B 2OUL_B 2FO8_A 2WGN_B 2C34_A ....
Probab=73.59 E-value=11 Score=20.27 Aligned_cols=18 Identities=17% Similarity=0.242 Sum_probs=14.7
Q ss_pred EEEecCCEEEEEEEeCCC
Q psy88 5 KNVCEGDRVVVDVRNSMD 22 (75)
Q Consensus 5 i~~~~Gd~v~i~~~N~~~ 22 (75)
|.++.||.+.|.|.-+..
T Consensus 1 I~v~~g~~~~I~L~~nps 18 (92)
T PF09394_consen 1 ITVKVGDTFEIELPENPS 18 (92)
T ss_dssp -EEETTSEEEEEEEEBCC
T ss_pred CeecCCCEEEEEECCCCC
Confidence 689999999999997644
No 86
>cd05468 pVHL von Hippel-Landau (pVHL) tumor suppressor protein. von Hippel-Landau (pVHL) protein, the gene product of VHL, is a critical regulator of the ubiquitous oxygen-sensing pathway. It is conserved throughout evolution, as its homologs are found in organisms ranging from mammals to the Drosophila melanogaster, Anopheles gambiae insects and the Caenorhabditis elegans nematode. pVHL acts as the substrate recognition component of an E3 ubiquitin ligase complex. Several proteins have been identified as pVHL-binding proteins that are subject to ubiquitin-mediated proteolysis; the best characterized putative substrates are the alpha subunits of the hypoxia-inducible factor (HIF1alpha, HIF2alpha, and HIF3alpha). In addition to HIF degradation, pVHL has been implicated to be involved in HIF independent cellular processes. Germline VHL mutations cause renal cell carcinomas, hemangioblastomas and pheochromocytomas in humans. pVHL can bind to and direct the proper deposition of fibronecti
Probab=72.55 E-value=14 Score=22.18 Aligned_cols=43 Identities=28% Similarity=0.375 Sum_probs=29.3
Q ss_pred ecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEE
Q psy88 8 CEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRY 60 (75)
Q Consensus 8 ~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y 60 (75)
+.+..+.|.|.|..+ .+.-+-| +.+ +|.. .....+.||++++.
T Consensus 4 ~s~~~~~v~F~N~t~-~~v~~~W--id~------~G~~-~~Y~~l~pg~~~~~ 46 (141)
T cd05468 4 NSRVPSTVRFVNRTD-RPVELYW--IDY------DGKP-VSYGTLQPGETVRQ 46 (141)
T ss_pred CCCceEEEEEEeCCC-CeEEEEE--ECC------CCCE-EEeeeeCCCCEEee
Confidence 456789999999998 7888887 322 3322 22344888888754
No 87
>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=71.27 E-value=18 Score=21.06 Aligned_cols=58 Identities=17% Similarity=0.361 Sum_probs=31.6
Q ss_pred EEecCCEEEEEEEeCCC--CC--CceEEe--CCccccCC-CCCCCCCcc-cccccCCCCEEEEEEc
Q psy88 6 NVCEGDRVVVDVRNSMD--GL--ENTIHW--HGIHQRGT-QYSDGVPFV-TQCPITQGNTFRYQFT 63 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~~~--~~--~~~iH~--HG~~~~~~-~~~DG~~~~-~~~~i~pG~~~~y~~~ 63 (75)
.+++|+.+.+.+.=... .. .+.+|+ -|+..+-. +..|+=... ..||+.+|+.++|...
T Consensus 25 ~l~rG~~~~~~i~F~~~~~~~~~~~~v~~~~~gv~ip~~~~~~daC~~~~~~CPl~~G~~~~y~~~ 90 (123)
T cd00916 25 KLKRGSTAKVSIDFTPNFDSTSLKTEVHAILLGVPVPFPLPNPDACKNLGTSCPLSAGEDVTYTLS 90 (123)
T ss_pred EEECCCEEEEEEEEEcCcccceeEEEEEEEECCEEecCCCCCCccccCCCCCCCCcCCcEEEEEEe
Confidence 46788888777662211 01 122222 24333211 124442111 4799999999999985
No 88
>MTH00098 COX2 cytochrome c oxidase subunit II; Validated
Probab=71.24 E-value=25 Score=22.81 Aligned_cols=56 Identities=7% Similarity=0.005 Sum_probs=35.6
Q ss_pred cEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEccC
Q psy88 4 PKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHAH 74 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~H 74 (75)
.|.+-.|..|++.++-..- | |+...+. -|+- . -.-||..-...+. +++|.|+.-|-
T Consensus 141 ~lvlP~~~~v~~~~tS~DV-----i--Hsf~ip~----lg~k---~-daiPG~~~~~~~~~~~~G~~~g~Cs 197 (227)
T MTH00098 141 RVVLPMEMPIRMLISSEDV-----L--HSWAVPS----LGLK---T-DAIPGRLNQTTLMSTRPGLYYGQCS 197 (227)
T ss_pred eEEecCCCEEEEEEEECcc-----c--ccccccc----cccc---e-ecCCCceEEEEEecCCcEEEEEECc
Confidence 4566667777777665432 2 5554442 2222 1 2458998888888 99999988773
No 89
>smart00110 C1Q Complement component C1q domain. Globular domain found in many collagens and eponymously in complement C1q. When part of full length proteins these domains form a 'bouquet' due to the multimerization of heterotrimers. The C1q fold is similar to that of tumour necrosis factor.
Probab=68.68 E-value=6.1 Score=23.51 Aligned_cols=16 Identities=19% Similarity=0.302 Sum_probs=14.0
Q ss_pred ccEEEecCCEEEEEEE
Q psy88 3 YPKNVCEGDRVVVDVR 18 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~ 18 (75)
..|.+++||+|.|++.
T Consensus 96 ~vL~L~~GD~Vwl~l~ 111 (135)
T smart00110 96 ALLQLRQGDQVWLELP 111 (135)
T ss_pred EEEEECCCCEEEEEEe
Confidence 4689999999999985
No 90
>PF09962 DUF2196: Uncharacterized conserved protein (DUF2196); InterPro: IPR019240 A pair of adjacent genes, ablAB (acetyl-beta-lysine biosynthesis) encodes lysine 2,3-aminomutase and beta-lysine acetyltransferase in methanogenic archaea. Homologous pairs, possibly with identical function, occur in a wide range of species, including Bacillus subtilis. This model describes a conserved hypothetical protein, small in size, with a phylogenetic distribution moderately well correlated to that of the acetyltransferase family. This protein family is also described as DUF2196 and COG4895 from COG. The function is unknown.
Probab=65.67 E-value=6.1 Score=20.80 Aligned_cols=36 Identities=25% Similarity=0.303 Sum_probs=25.1
Q ss_pred EecCCEEEEEEEeCCCC------------CCceEEeCCccccCCCCCCCCC
Q psy88 7 VCEGDRVVVDVRNSMDG------------LENTIHWHGIHQRGTQYSDGVP 45 (75)
Q Consensus 7 ~~~Gd~v~i~~~N~~~~------------~~~~iH~HG~~~~~~~~~DG~~ 45 (75)
++.|..|.|.+++.-.. ...+.|.||+...- .||.-
T Consensus 9 I~~G~~V~IVlK~dQ~tg~lt~GiV~~iLT~s~~HP~GIKVrL---~~G~V 56 (62)
T PF09962_consen 9 IKPGITVEIVLKQDQRTGKLTEGIVKDILTNSPTHPHGIKVRL---EDGQV 56 (62)
T ss_pred ccCCCEEEEEECCCCCcCccccEEhheeecCCCCCCCCcEEEe---cCCCe
Confidence 57899999988886431 13568999988764 36643
No 91
>MTH00129 COX2 cytochrome c oxidase subunit II; Provisional
Probab=65.58 E-value=35 Score=22.21 Aligned_cols=56 Identities=16% Similarity=0.121 Sum_probs=36.1
Q ss_pred cEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEccC
Q psy88 4 PKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHAH 74 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~H 74 (75)
.+.+-.|..+++.++-.. .| |+...+. -|.. ...-||..-...+. +++|+|+--|.
T Consensus 141 ~lvlP~~~~v~~~~tS~D-----Vi--Hsf~ip~----~~~k----~da~PG~~~~~~~~~~~~G~~~g~C~ 197 (230)
T MTH00129 141 RMVVPVESPIRVLVSAED-----VL--HSWAVPA----LGVK----MDAVPGRLNQTAFIASRPGVFYGQCS 197 (230)
T ss_pred eEEEecCcEEEEEEEeCc-----cc--cceeccc----cCCc----cccCCCceEEEEEEeCCceEEEEECh
Confidence 466667777777776543 22 5554442 2221 12558999888888 99999988773
No 92
>MTH00051 COX2 cytochrome c oxidase subunit II; Provisional
Probab=65.07 E-value=36 Score=22.20 Aligned_cols=55 Identities=16% Similarity=0.073 Sum_probs=37.0
Q ss_pred cEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEcc
Q psy88 4 PKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHA 73 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~ 73 (75)
.|.+-.|+.+++.+++..- | |+...+. -|.- .-.-||..-...+. +++|+|.--|
T Consensus 145 ~lvlP~~~~v~~~itS~DV-----i--Hsf~vp~----lg~k----~daiPG~~~~~~~~~~~~G~y~g~C 200 (234)
T MTH00051 145 RLIVPIQTQVRVLVTAADV-----L--HSFAVPS----LSVK----IDAVPGRLNQTSFFIKRPGVFYGQC 200 (234)
T ss_pred EEEEecCcEEEEEEEeCch-----h--ccccccc----cCce----eEccCCceEeEEEEeCCCEEEEEEC
Confidence 4777889999999888632 2 5554432 2222 12458888888888 9999988766
No 93
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=64.60 E-value=7.7 Score=20.73 Aligned_cols=16 Identities=25% Similarity=0.391 Sum_probs=13.4
Q ss_pred cEEEecCCEEEEEEEe
Q psy88 4 PKNVCEGDRVVVDVRN 19 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N 19 (75)
-|++.+||.|.|.+.-
T Consensus 42 rI~I~~GD~V~Ve~sp 57 (68)
T TIGR00008 42 YIRILPGDKVKVELSP 57 (68)
T ss_pred cEEECCCCEEEEEECc
Confidence 5789999999998754
No 94
>TIGR03833 conserved hypothetical protein. A pair of adjacent genes, ablAB (acetyl-beta-lysine biosynthesis) encodes lysine 2,3-aminomutase and beta-lysine acetyltransferase in methanogenic archaea. Homologous pairs, possibly with identical function, occur in a wide range of species, including Bacillus subtilis. This model describes a conserved hypothetical protein, small in size, with a phylogenetic distribution moderately well correlated to that of the acetyltransferase family. This protein family is also described as DUF2196 and COG4895. The function is unknown.
Probab=63.17 E-value=8.2 Score=20.30 Aligned_cols=37 Identities=27% Similarity=0.319 Sum_probs=24.9
Q ss_pred EEecCCEEEEEEEeCCCC------------CCceEEeCCccccCCCCCCCCC
Q psy88 6 NVCEGDRVVVDVRNSMDG------------LENTIHWHGIHQRGTQYSDGVP 45 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~~~~------------~~~~iH~HG~~~~~~~~~DG~~ 45 (75)
.++.|..|.|.++..-.. ...+.|.||+.+.- .||.-
T Consensus 7 ~I~~G~~V~IvlK~DQ~tG~lt~G~V~diLT~s~~Hp~GIKVrL---~dG~V 55 (62)
T TIGR03833 7 NIKPGLSVDIVLKQDQRTGKLTRGIVKDILTNSPTHPHGIKVRL---EDGQV 55 (62)
T ss_pred ccCCCCEEEEEEeccCCCCceeeEEhhhhhcCCCCCCCceEEEE---ecCCe
Confidence 356788999988864321 13578999998764 47643
No 95
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=62.72 E-value=8.6 Score=21.59 Aligned_cols=28 Identities=18% Similarity=0.143 Sum_probs=18.6
Q ss_pred cEEEecCCEEEEEEEeCCCCCCceEEeC
Q psy88 4 PKNVCEGDRVVVDVRNSMDGLENTIHWH 31 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~~~~~~iH~H 31 (75)
-|++..||.|.|.+.--.....-.++-|
T Consensus 44 rIrIl~GD~V~VE~spYDltkGRIiyR~ 71 (87)
T PRK12442 44 RIRILAGDRVTLELSPYDLTKGRINFRH 71 (87)
T ss_pred eEEecCCCEEEEEECcccCCceeEEEEe
Confidence 4889999999999885433233344444
No 96
>KOG4387|consensus
Probab=62.57 E-value=3.4 Score=26.31 Aligned_cols=30 Identities=13% Similarity=0.452 Sum_probs=23.9
Q ss_pred EEEecCCEEEEEEEeCCCCCCceEEeCCccc
Q psy88 5 KNVCEGDRVVVDVRNSMDGLENTIHWHGIHQ 35 (75)
Q Consensus 5 i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~ 35 (75)
...+.++.+.+.+.|.+. ...+++|||+.-
T Consensus 71 ~~~n~~~~~~~d~~~rlt-~~~s~~W~~vl~ 100 (191)
T KOG4387|consen 71 LPGNDRKPGILDFQERLT-VAKSMNWHGVLS 100 (191)
T ss_pred ccccCCCCcEEeccchhh-eeeecccceEEe
Confidence 345567888899999988 789999999753
No 97
>KOG4063|consensus
Probab=61.32 E-value=35 Score=21.22 Aligned_cols=16 Identities=25% Similarity=0.802 Sum_probs=14.4
Q ss_pred cccccCCCCEEEEEEc
Q psy88 48 TQCPITQGNTFRYQFT 63 (75)
Q Consensus 48 ~~~~i~pG~~~~y~~~ 63 (75)
..||+.+||.++|.+.
T Consensus 106 v~CPl~age~ytY~~s 121 (158)
T KOG4063|consen 106 VYCPLSAGEDYTYLNS 121 (158)
T ss_pred ccCcccCCCceEEEEE
Confidence 4799999999999976
No 98
>MTH00008 COX2 cytochrome c oxidase subunit II; Validated
Probab=61.23 E-value=43 Score=21.77 Aligned_cols=55 Identities=18% Similarity=0.144 Sum_probs=36.7
Q ss_pred cEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEcc
Q psy88 4 PKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHA 73 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~ 73 (75)
.+.+-.|..|++.+++..- | |+...+. -|.- ...-||..-...+. +++|.|+--|
T Consensus 141 ~lvlP~~~~v~~~~tS~DV-----i--Hsf~vP~----~~~k----~daiPG~~~~~~~~~~~~G~~~g~C 196 (228)
T MTH00008 141 RAVLPMQTEIRVLVTAADV-----I--HSWTVPS----LGVK----VDAVPGRLNQIGFTITRPGVFYGQC 196 (228)
T ss_pred eEEEecCCEEEEEEEeCCc-----c--ccccccc----cCcc----eecCCCceEEEEEEeCCCEEEEEEC
Confidence 5667788888998888532 2 5554432 2221 12458888888888 9999988766
No 99
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=60.89 E-value=9.9 Score=20.74 Aligned_cols=17 Identities=24% Similarity=0.350 Sum_probs=13.9
Q ss_pred cEEEecCCEEEEEEEeC
Q psy88 4 PKNVCEGDRVVVDVRNS 20 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~ 20 (75)
-|++.+||.|.|.+.--
T Consensus 44 ~i~I~~GD~V~Ve~~~~ 60 (75)
T COG0361 44 RIRILPGDVVLVELSPY 60 (75)
T ss_pred eEEeCCCCEEEEEeccc
Confidence 58899999999987643
No 100
>KOG2500|consensus
Probab=59.45 E-value=7.3 Score=25.73 Aligned_cols=18 Identities=17% Similarity=0.399 Sum_probs=15.0
Q ss_pred cEEEecCCEEEEEEEeCC
Q psy88 4 PKNVCEGDRVVVDVRNSM 21 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~ 21 (75)
-+-+|+|++|+|.+.|..
T Consensus 149 DlgFKEGeTIkinikn~t 166 (253)
T KOG2500|consen 149 DLGFKEGETIKINIKNIT 166 (253)
T ss_pred cccccCCcEEEEEeeccc
Confidence 356899999999999843
No 101
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=58.85 E-value=6.3 Score=22.68 Aligned_cols=17 Identities=24% Similarity=0.190 Sum_probs=14.4
Q ss_pred EEecCCEEEEEEEeCCC
Q psy88 6 NVCEGDRVVVDVRNSMD 22 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~~~ 22 (75)
.++.||.|+|++.|..-
T Consensus 48 ~VK~GD~l~i~~~~~~~ 64 (100)
T COG1188 48 EVKVGDILTIRFGNKEF 64 (100)
T ss_pred ccCCCCEEEEEeCCcEE
Confidence 47899999999999853
No 102
>PF12306 PixA: Inclusion body protein; InterPro: IPR021087 This entry represents bacterial proteins that are typically between 173 and 191 amino acids in length. PixA is thought to be specifically produced in Xenorhabdus nematophila. It is an inclusion body protein []. This signature also identifies AidA.
Probab=58.39 E-value=42 Score=20.80 Aligned_cols=18 Identities=11% Similarity=0.067 Sum_probs=15.3
Q ss_pred ccEEEecCCEEEEEEEeC
Q psy88 3 YPKNVCEGDRVVVDVRNS 20 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N~ 20 (75)
+.|+++.||.|+++..--
T Consensus 58 L~i~a~~GD~Irwr~tSl 75 (172)
T PF12306_consen 58 LSIKANVGDTIRWRATSL 75 (172)
T ss_pred eEEeccCCCEEEEEEEee
Confidence 578999999999998744
No 103
>cd08058 MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); eukaryotic. This family contains eukaryotic MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in proteins with a variety of functions, including AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM), H2A-DUB (histone H2A deubiquitinase), BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as well as Rpn11 (regulatory particle number 11) and CSN5 (COP9 signalosome complex subunit 5). These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology. CSN5 is critical for nuclear export and the degradation of several tumor suppressor prot
Probab=57.89 E-value=5.1 Score=23.01 Aligned_cols=7 Identities=29% Similarity=0.928 Sum_probs=5.5
Q ss_pred eEEccCC
Q psy88 69 HFWHAHT 75 (75)
Q Consensus 69 ~~YH~H~ 75 (75)
=|||||.
T Consensus 69 G~YHSHP 75 (119)
T cd08058 69 GWYHSHP 75 (119)
T ss_pred EEEecCC
Confidence 3999994
No 104
>PRK12791 flbT flagellar biosynthesis repressor FlbT; Reviewed
Probab=57.38 E-value=9.7 Score=22.89 Aligned_cols=27 Identities=19% Similarity=0.178 Sum_probs=19.5
Q ss_pred CcccEEEecCCEEEEE---EEeCCCCCCceEE
Q psy88 1 MLYPKNVCEGDRVVVD---VRNSMDGLENTIH 29 (75)
Q Consensus 1 ~~~~i~~~~Gd~v~i~---~~N~~~~~~~~iH 29 (75)
|++.|.+|.|+++.|. +.|.. +..++-
T Consensus 1 M~Lkl~LKP~ERi~INGaVi~Ngd--rr~~l~ 30 (131)
T PRK12791 1 MPLRVELKPFERIVIGQSVITNSD--TRARFL 30 (131)
T ss_pred CCeeEEeCCCCEEEEcCEEEEeCC--cceEEE
Confidence 8899999999999884 55553 344443
No 105
>PF00927 Transglut_C: Transglutaminase family, C-terminal ig like domain; InterPro: IPR008958 Synonym(s): Protein-glutamine gamma-glutamyltransferase, Fibrinoligase, TGase Transglutaminases catalyse the post-translational modification of proteins at glutamine residues, with formation of isopeptide bonds. Members of the transglutaminase family usually have three domains: N-terminal (IPR001102 from INTERPRO), middle (IPR013808 from INTERPRO) and C-terminal. The middle domain is usually well conserved, but family members can display major differences in their N- and C-terminal domains, although their overall structure is conserved []. This entry represents the C-terminal domain found in transglutaminases, which consists of an immunoglobulin-like beta-sandwich consisting of seven strands in two sheets with a Greek key topology. 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. Protein-glutamine gamma-glutamyltransferases (2.3.2.13 from EC) 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 [, ].; GO: 0003810 protein-glutamine gamma-glutamyltransferase activity, 0018149 peptide cross-linking; PDB: 2XZZ_A 1GGY_B 1FIE_B 1GGU_B 1GGT_B 1F13_A 1QRK_B 1EVU_A 1EX0_B 1L9N_B ....
Probab=57.23 E-value=7.3 Score=21.80 Aligned_cols=19 Identities=21% Similarity=0.331 Sum_probs=13.5
Q ss_pred cccCCCCEEEEEEc---CCCee
Q psy88 50 CPITQGNTFRYQFT---ANAGT 68 (75)
Q Consensus 50 ~~i~pG~~~~y~~~---~~~Gt 68 (75)
..|.||++.++++. .+.|.
T Consensus 60 ~~l~p~~~~~~~~~i~p~~yG~ 81 (107)
T PF00927_consen 60 VTLKPGETKSVEVTITPSQYGP 81 (107)
T ss_dssp EEE-TTEEEEEEEEE-HHSHEE
T ss_pred eeeCCCCEEEEEEEEEceeEec
Confidence 34899999999988 45553
No 106
>COG2880 Uncharacterized protein conserved in archaea [Function unknown]
Probab=54.96 E-value=11 Score=20.22 Aligned_cols=19 Identities=26% Similarity=0.378 Sum_probs=16.1
Q ss_pred CcccEEEecCCEEEEEEEe
Q psy88 1 MLYPKNVCEGDRVVVDVRN 19 (75)
Q Consensus 1 ~~~~i~~~~Gd~v~i~~~N 19 (75)
+++.+.+++|+.|+|.+.|
T Consensus 18 PLqkv~LkEGekv~i~i~~ 36 (67)
T COG2880 18 PLKKVDLKEGEKVKIVIRV 36 (67)
T ss_pred ccccccCCCCCEEEEEEec
Confidence 4678899999999999855
No 107
>PF05688 DUF824: Salmonella repeat of unknown function (DUF824); InterPro: IPR008542 This family consists of a series of repeated sequences (of around 180 residues) which are found in Salmonella typhimurium, Salmonella typhi and Escherichia coli. These repeats are almost always found with this entry. The repeats are associated with RatA and RatB, the coding sequences of which are found in the pathogeneicity island of Salmonella. The sequences may be determinants of pathogenicity [, ].
Probab=54.63 E-value=14 Score=18.28 Aligned_cols=15 Identities=13% Similarity=0.202 Sum_probs=11.7
Q ss_pred EEEecCCEEEEEEEe
Q psy88 5 KNVCEGDRVVVDVRN 19 (75)
Q Consensus 5 i~~~~Gd~v~i~~~N 19 (75)
..+|.||+|.+++.=
T Consensus 7 akaK~Ge~I~ltVt~ 21 (47)
T PF05688_consen 7 AKAKVGETIPLTVTV 21 (47)
T ss_pred hheecCCeEEEEEEE
Confidence 468999998887763
No 108
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=51.39 E-value=9.4 Score=18.77 Aligned_cols=15 Identities=20% Similarity=0.038 Sum_probs=10.7
Q ss_pred cccEEEecCCEEEEE
Q psy88 2 LYPKNVCEGDRVVVD 16 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~ 16 (75)
+..|.+++||.|+|.
T Consensus 13 ~~~Ls~~~Gd~i~v~ 27 (55)
T PF07653_consen 13 PDELSFKKGDVIEVL 27 (55)
T ss_dssp TTB-EB-TTEEEEEE
T ss_pred CCceEEecCCEEEEE
Confidence 356899999999987
No 109
>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=51.26 E-value=14 Score=21.33 Aligned_cols=16 Identities=31% Similarity=0.856 Sum_probs=14.1
Q ss_pred cccccCCCCEEEEEEc
Q psy88 48 TQCPITQGNTFRYQFT 63 (75)
Q Consensus 48 ~~~~i~pG~~~~y~~~ 63 (75)
..||+.+|+.++|...
T Consensus 78 ~~CPl~~G~~~~~~~~ 93 (127)
T cd00912 78 SFCPLRKGQQYSYAKT 93 (127)
T ss_pred ccCCcCCCCEEEEEEE
Confidence 3699999999999986
No 110
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=50.36 E-value=19 Score=19.56 Aligned_cols=17 Identities=24% Similarity=0.239 Sum_probs=14.0
Q ss_pred cEEEecCCEEEEEEEeC
Q psy88 4 PKNVCEGDRVVVDVRNS 20 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~ 20 (75)
.|++++||.|.|...-.
T Consensus 36 ~iwI~~GD~VlV~~~~~ 52 (78)
T cd04456 36 NIWIKRGDFLIVDPIEE 52 (78)
T ss_pred CEEEcCCCEEEEEeccc
Confidence 48999999999986553
No 111
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=50.00 E-value=19 Score=19.47 Aligned_cols=17 Identities=29% Similarity=0.235 Sum_probs=13.9
Q ss_pred cEEEecCCEEEEEEEeC
Q psy88 4 PKNVCEGDRVVVDVRNS 20 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~ 20 (75)
.|++++||.|.|.+.-.
T Consensus 36 ~iwI~~GD~V~Ve~~~~ 52 (77)
T cd05793 36 RVWINEGDIVLVAPWDF 52 (77)
T ss_pred cEEEcCCCEEEEEeccc
Confidence 58999999999986544
No 112
>TIGR01432 QOXA cytochrome aa3 quinol oxidase, subunit II. This enzyme catalyzes the oxidation of quinol with the concomitant reduction of molecular oxygen to water. This acts as the terminal electron acceptor in the respiratory chain. This subunit contains two transmembrane helices and a large external domain responsible for the binding and oxidation of quinol. QuoX is (presently) only found in gram positive bacteria of the Bacillus/Staphylococcus group. Like CyoA, the ubiquinol oxidase found in proteobacteria, the residues responsible for the ligation of Cu(a) and cytochrome c (found in the related cyt. c oxidases) are absent. Unlike CyoA, QoxA is in complex with a subunit I which contains cytochromes a similar to the cyt. c oxidases (as opposed to cytochromes b).
Probab=49.93 E-value=66 Score=20.56 Aligned_cols=56 Identities=16% Similarity=0.129 Sum_probs=36.4
Q ss_pred ccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEcc
Q psy88 3 YPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHA 73 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~ 73 (75)
..|.+-.|..|++.++... .| |.+..+.. -+ +.-.-||..-...|. +++|+|.=.|
T Consensus 130 n~l~iP~g~~v~~~ltS~D-----Vi--Hsf~vP~l---~~-----k~daiPG~~~~~~~~~~~~G~y~g~C 186 (217)
T TIGR01432 130 NYLNIPKDRPVLFKLQSAD-----TM--TSFWIPQL---GG-----QKYAMTGMTMNWYLQADQVGTYRGRN 186 (217)
T ss_pred CcEEEECCCEEEEEEECCc-----hh--hhhhchhh---Cc-----eeecCCCceEEEEEEeCCCEEEEEEe
Confidence 3577788888888887653 22 44444321 11 112458888888888 9999997666
No 113
>MTH00185 COX2 cytochrome c oxidase subunit II; Provisional
Probab=49.69 E-value=71 Score=20.80 Aligned_cols=56 Identities=14% Similarity=0.100 Sum_probs=35.1
Q ss_pred cEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEccC
Q psy88 4 PKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHAH 74 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~H 74 (75)
.+.+-.|..+++.++-.. .| |+...+. -|.- ...-||+.....+. +++|+|.--|.
T Consensus 141 ~lvlP~~~~v~~~~tS~D-----Vi--Hsf~iP~----lg~k----~daiPG~~~~~~~~~~~~G~~~g~Cs 197 (230)
T MTH00185 141 RMVVPMESPIRVLITAED-----VL--HSWTVPA----LGVK----MDAVPGRLNQATFIISRPGLYYGQCS 197 (230)
T ss_pred eEEEecCCEEEEEEEcCc-----cc--ccccccc----cCce----eEecCCceEEEEEEeCCcEEEEEEch
Confidence 456666777777766543 22 5554442 2222 12458888888888 99999987763
No 114
>PF01847 VHL: von Hippel-Lindau disease tumour suppressor protein; InterPro: IPR022772 Von Hippel-Lindau disease tumor suppressor (VHL) has two domains: a roughly 100-residue N-terminal domain rich in beta sheet (beta domain) and a smaller alpha-helical domain (alpha domain), held together by two linkers and a polar interface. A large portion of the alpha domain surface, and a small portion of the beta domain, interact with ElonginC. About half of the tumorigenic mutations map to the alpha domain and its residues that contact ElonginC. The remaining mutations map to the beta domain, and significantly, to a beta domain surface patch uninvolved in ElonginC binding. This suggests that two intact macromolecular binding sites may be required for the tumor suppressor effects of VHL []. This entry represents both beta and alpha domains of VHL.; PDB: 3ZRF_L 3ZRC_C 1LM8_V 1LQB_C 1VCB_F.
Probab=49.63 E-value=35 Score=21.20 Aligned_cols=45 Identities=18% Similarity=0.245 Sum_probs=24.2
Q ss_pred EecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEE
Q psy88 7 VCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQ 61 (75)
Q Consensus 7 ~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~ 61 (75)
++..+...|.|.|..+ ...-+-|=. .||.+. ....+.||+.+...
T Consensus 9 ~~S~~~s~V~F~N~s~-r~V~v~Wld--------y~G~~~-~Y~~L~Pg~~~~~~ 53 (156)
T PF01847_consen 9 LNSREPSFVRFVNRSP-RTVDVYWLD--------YDGKPV-PYGTLKPGQGRRQN 53 (156)
T ss_dssp ----SEEEEEEEE-SS-S-EEEEEE---------TTS-EE-E---B-TTEEEEEE
T ss_pred CCCCCceEEEEEECCC-CEEEEEEEc--------CCCcEe-eccccCCCCeEEcc
Confidence 3456789999999998 788888822 245332 12348899887764
No 115
>PF05753 TRAP_beta: Translocon-associated protein beta (TRAPB); InterPro: IPR008856 This family consists of several eukaryotic translocon-associated protein beta (TRAPB) or signal sequence receptor beta subunit (SSR-beta) proteins. The normal translocation of nascent polypeptides into the lumen of the endoplasmic reticulum (ER) is thought to be aided in part by a translocon-associated protein (TRAP) complex consisting of 4 protein subunits. The association of mature proteins with the ER and Golgi, or other intracellular locales, such as lysosomes, depends on the initial targeting of the nascent polypeptide to the ER membrane. A similar scenario must also exist for proteins destined for secretion [].; GO: 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=49.15 E-value=65 Score=20.23 Aligned_cols=21 Identities=14% Similarity=0.230 Sum_probs=15.7
Q ss_pred ccccCCCCEEEEEEc---CCCeee
Q psy88 49 QCPITQGNTFRYQFT---ANAGTH 69 (75)
Q Consensus 49 ~~~i~pG~~~~y~~~---~~~Gt~ 69 (75)
-..|+||++.+..+. ...|.|
T Consensus 80 ~~~i~pg~~vsh~~vv~p~~~G~f 103 (181)
T PF05753_consen 80 WERIPPGENVSHSYVVRPKKSGYF 103 (181)
T ss_pred EEEECCCCeEEEEEEEeeeeeEEE
Confidence 356899999988887 446655
No 116
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=49.15 E-value=26 Score=20.51 Aligned_cols=17 Identities=18% Similarity=0.366 Sum_probs=14.4
Q ss_pred EEecCCEEEEEEEeCCC
Q psy88 6 NVCEGDRVVVDVRNSMD 22 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~~~ 22 (75)
.++.||+|+++|....+
T Consensus 88 ~lk~G~~V~F~~~~~~~ 104 (115)
T PRK09838 88 EIKTGDKVAFNFVQQGN 104 (115)
T ss_pred cCCCCCEEEEEEEEcCC
Confidence 46899999999998765
No 117
>cd07700 IgV_CD8_beta Immunoglobulin (Ig) like domain of CD8 beta chain. IgV_CD8_beta: immunoglobulin (Ig)-like domain in CD8 beta. The CD8 glycoprotein plays an essential role in the control of T-cell selection, maturation and the T-cell receptor (TCR)-mediated response to peptide antigen. CD8 is comprised of alpha and beta subunits and is expressed as either an alpha/alpha or alpha/beta dimer. Both dimeric isoforms can serve as a coreceptor for T cell activation and differentiation, however they have distinct physiological roles, different cellular distributions, unique binding partners etc. Each CD8 subunit is comprised of an extracellular domain containing a V-type Ig-like domain, a single pass transmembrane portion and a short intracellular domain.
Probab=49.10 E-value=33 Score=18.96 Aligned_cols=27 Identities=15% Similarity=0.101 Sum_probs=18.7
Q ss_pred EEEecCCEEEEEEEeCCCCCCceEEeC
Q psy88 5 KNVCEGDRVVVDVRNSMDGLENTIHWH 31 (75)
Q Consensus 5 i~~~~Gd~v~i~~~N~~~~~~~~iH~H 31 (75)
|.+++|++|+|.=..........++|-
T Consensus 1 ~~v~~G~~vtL~C~~~~~~~~~~~~Wy 27 (107)
T cd07700 1 ILVQTNNTVKLSCEAKGISENTRIYWL 27 (107)
T ss_pred CEEcCCCCEEEEEEEecCCCCCeEEEE
Confidence 568999999999765331135578883
No 118
>PF14646 MYCBPAP: MYCBP-associated protein family
Probab=48.68 E-value=63 Score=22.76 Aligned_cols=61 Identities=21% Similarity=0.260 Sum_probs=35.9
Q ss_pred cEEEecCCEEE--EE-EEeCCCCCCceEEeCCccccCCC-----------CCCCCCcccccccCCCCEEEEEEc---CCC
Q psy88 4 PKNVCEGDRVV--VD-VRNSMDGLENTIHWHGIHQRGTQ-----------YSDGVPFVTQCPITQGNTFRYQFT---ANA 66 (75)
Q Consensus 4 ~i~~~~Gd~v~--i~-~~N~~~~~~~~iH~HG~~~~~~~-----------~~DG~~~~~~~~i~pG~~~~y~~~---~~~ 66 (75)
++.+..|+.+. |. |.|... ......|.=+...... ..|-. .-.|.||++..+.|. ..+
T Consensus 240 ~Fe~~p~e~~~~~v~~l~N~Gt-~~I~y~W~~~~~~~~~~~~~~~~~~~F~Fd~~----~gvilPGe~~~~~~~F~s~~~ 314 (426)
T PF14646_consen 240 TFECHPGERVSKEVVRLENNGT-TAIYYSWRRVPFFKNFGSLFRAQDQRFYFDTS----SGVILPGETRNFPFMFKSRKV 314 (426)
T ss_pred EEEcccCceeeEEEEEEecCCc-eEEEEEEEecccccccchhccccCCeEEEeCC----CCEECCCceEEEEEEEeCCCc
Confidence 44555665543 33 778876 5666677655442110 01111 223899999999887 678
Q ss_pred eee
Q psy88 67 GTH 69 (75)
Q Consensus 67 Gt~ 69 (75)
|.|
T Consensus 315 Gif 317 (426)
T PF14646_consen 315 GIF 317 (426)
T ss_pred eEE
Confidence 865
No 119
>TIGR01433 CyoA cytochrome o ubiquinol oxidase subunit II. This enzyme catalyzes the oxidation of ubiquinol with the concomitant reduction of molecular oxygen to water. This acts as the terminal electron acceptor in the respiratory chain. Subunit II is responsible for binding and oxidation of the ubiquinone substrate. This sequence is closely related to QoxA, which oxidizes quinol in gram positive bacteria but which is in complex with subunits which utilize cytochromes a in the reduction of molecular oxygen. Slightly more distantly related is subunit II of cytochrome c oxidase which uses cyt. c as the oxidant.
Probab=48.48 E-value=74 Score=20.66 Aligned_cols=56 Identities=4% Similarity=-0.044 Sum_probs=36.3
Q ss_pred ccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEcc
Q psy88 3 YPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHA 73 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~ 73 (75)
..|++-.|..|++.++-.. .| |++..+.. -+ .+ -.-||..-...|. +++|+|.-.|
T Consensus 139 nel~lP~g~pV~~~ltS~D-----Vi--HSF~VP~l---~~----K~-DaiPG~~n~~~~~~~~~G~y~g~C 195 (226)
T TIGR01433 139 NEIAFPVNTPINFKITSNS-----VM--NSFFIPQL---GS----QI-YAMAGMQTKLHLIANEPGVYDGIS 195 (226)
T ss_pred ceEEEECCCEEEEEEEECc-----hh--hhhhhhhc---CC----ee-ecCCCceEEEEEEeCCCEEEEEEc
Confidence 4678888999998887763 22 44443321 11 11 1447888888888 9999987666
No 120
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=47.92 E-value=25 Score=18.86 Aligned_cols=16 Identities=31% Similarity=0.376 Sum_probs=13.6
Q ss_pred EecCCEEEEEEEeCCC
Q psy88 7 VCEGDRVVVDVRNSMD 22 (75)
Q Consensus 7 ~~~Gd~v~i~~~N~~~ 22 (75)
.+.||+|++.++.+-+
T Consensus 3 ~~~Ge~v~~~~~~~~~ 18 (83)
T PF14326_consen 3 YRVGERVRFRVTSNRD 18 (83)
T ss_pred ccCCCEEEEEEEeCCC
Confidence 5789999999998754
No 121
>PF04744 Monooxygenase_B: Monooxygenase subunit B protein; InterPro: IPR006833 Ammonia monooxygenase and the particulate methane monooxygenase are both integral membrane proteins, occurring in ammonia oxidisers and methanotrophs respectively, which are thought to be evolutionarily related []. These enzymes have a relatively wide substrate specificity and can catalyse the oxidation of a range of substrates including ammonia, methane, halogenated hydrocarbons and aromatic molecules []. These enzymes are composed of 3 subunits - A (IPR003393 from INTERPRO), B (IPR006833 from INTERPRO) and C (IPR006980 from INTERPRO) - and contain various metal centres, including copper. Particulate methane monooxygenase from Methylococcus capsulatus str. Bath is an ABC homotrimer, which contains mononuclear and dinuclear copper metal centres, and a third metal centre containing a metal ion whose identity in vivo is not certain[]. The soluble regions of these enzymes derive primarily from the B subunit. This subunit forms two antiparallel beta-barrel-like structures and contains the mono- and di- nuclear copper metal centres [].; PDB: 3CHX_E 3RFR_A 3RGB_A 1YEW_A.
Probab=47.35 E-value=18 Score=25.53 Aligned_cols=34 Identities=21% Similarity=0.506 Sum_probs=18.9
Q ss_pred CCCCCCcccccccCCCCEEEEEEc---CCCeeeEEcc
Q psy88 40 YSDGVPFVTQCPITQGNTFRYQFT---ANAGTHFWHA 73 (75)
Q Consensus 40 ~~DG~~~~~~~~i~pG~~~~y~~~---~~~Gt~~YH~ 73 (75)
|..|.+...-..+..|+.+.|++. ..||+|.-|.
T Consensus 71 ~ing~~~p~S~~le~G~~y~fki~lkar~pG~~hvh~ 107 (381)
T PF04744_consen 71 WINGQPVPRSVSLELGGTYEFKIVLKARRPGTWHVHP 107 (381)
T ss_dssp EETTEE-SS-B---TT-EEEEEEEEEE-S-EEEEEEE
T ss_pred eecCccccceEEeecCCeeeEEEEEecccCcccccee
Confidence 345544333456889999999987 7899998875
No 122
>PF00207 A2M: Alpha-2-macroglobulin family; InterPro: IPR001599 This entry contains serum complement C3 and C4 precursors and alpha-macrogrobulins. The alpha-macroglobulin (aM) family of proteins includes protease inhibitors [], typified by the human tetrameric a2-macroglobulin (a2M); they belong to the MEROPS proteinase inhibitor family I39, clan IL. These protease inhibitors share several defining properties, which include (i) the ability to inhibit proteases from all catalytic classes, (ii) the presence of a 'bait region' and a thiol ester, (iii) a similar protease inhibitory mechanism and (iv) the inactivation of the inhibitory capacity by reaction of the thiol ester with small primary amines. aM protease inhibitors inhibit by steric hindrance []. The mechanism involves protease cleavage of the bait region, a segment of the aM that is particularly susceptible to proteolytic cleavage, which initiates a conformational change such that the aM collapses about the protease. In the resulting aM-protease complex, the active site of the protease is sterically shielded, thus substantially decreasing access to protein substrates. Two additional events occur as a consequence of bait region cleavage, namely (i) the h-cysteinyl-g-glutamyl thiol ester becomes highly reactive and (ii) a major conformational change exposes a conserved COOH-terminal receptor binding domain [] (RBD). RBD exposure allows the aM protease complex to bind to clearance receptors and be removed from circulation []. Tetrameric, dimeric, and, more recently, monomeric aM protease inhibitors have been identified [, ].; GO: 0004866 endopeptidase inhibitor activity; PDB: 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 2PN5_A 3FRP_G 3HRZ_B ....
Probab=47.29 E-value=37 Score=18.43 Aligned_cols=19 Identities=32% Similarity=0.600 Sum_probs=12.5
Q ss_pred cEEEecCCEEEEEE--EeCCC
Q psy88 4 PKNVCEGDRVVVDV--RNSMD 22 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~--~N~~~ 22 (75)
+-.+++||++.|.+ .|.++
T Consensus 63 P~~l~~GD~~~i~v~v~N~~~ 83 (92)
T PF00207_consen 63 PRSLRRGDQIQIPVTVFNYTD 83 (92)
T ss_dssp -SEEETTSEEEEEEEEEE-SS
T ss_pred CcEEecCCEEEEEEEEEeCCC
Confidence 44678999887654 58876
No 123
>cd08067 MPN_2A_DUB Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase. This family includes histone H2A deubiquitinase (Histone H2A DUB;MYSM1; myb-like, SWIRM and MPN domains 1; 2ADUB; 2A-DUB; KIAA19152ADUB, or KIAA1915/MYSM1), a member of JAMM/MPN+ deubiquitinases (DUBs), with possible Zn2+-dependent ubiquitin isopeptidase activity. It contains the SWIRM (Swi3p, Rsc8p and Moira), and SANT (SWI-SNF, ADA N-CoR, TFIIIB)/Myb domains; the SANT, but not the SWIRM, domain can bind directly to DNA. 2A-DUB is specific for monoubiquitinated H2A (uH2A), regulating transcription by coordinating histone acetylation and deubiquitination, and destabilizing the association of linker histone H1 with nucleosomes. 2A-DUB interacts with p/CAF (p300/CBP-associated factor) in a co-regulatory protein complex, where the status of acetylation of nucleosomal histones modulates its deubiquitinase activity. 2A-DUB is a positive regulator of androgen receptor (AR) transactivation activity on a reporter gene; it p
Probab=47.02 E-value=8.8 Score=24.23 Aligned_cols=7 Identities=29% Similarity=0.928 Sum_probs=5.6
Q ss_pred eEEccCC
Q psy88 69 HFWHAHT 75 (75)
Q Consensus 69 ~~YH~H~ 75 (75)
=|||||.
T Consensus 83 GwYHSHP 89 (187)
T cd08067 83 GWYHSHP 89 (187)
T ss_pred EEEecCC
Confidence 3999994
No 124
>PRK00794 flbT flagellar biosynthesis repressor FlbT; Reviewed
Probab=46.96 E-value=19 Score=21.66 Aligned_cols=29 Identities=17% Similarity=0.320 Sum_probs=21.0
Q ss_pred CcccEEEecCCEEEEE---EEeCCCCCCceEEeCC
Q psy88 1 MLYPKNVCEGDRVVVD---VRNSMDGLENTIHWHG 32 (75)
Q Consensus 1 ~~~~i~~~~Gd~v~i~---~~N~~~~~~~~iH~HG 32 (75)
|++.|.+|.|+++.|. +.| + +..++-.-+
T Consensus 2 ~~Lkl~LKp~ERi~INGAVirn--d-rr~~l~i~n 33 (132)
T PRK00794 2 SGLKLSLKPGERIFINGAVLRN--D-RKVSLELLN 33 (132)
T ss_pred CCeeEEecCCCEEEEcCeEEEe--C-CceEEEEec
Confidence 6889999999999884 667 4 455554433
No 125
>smart00207 TNF Tumour necrosis factor family. Family of cytokines that form homotrimeric or heterotrimeric complexes. TNF mediates mature T-cell receptor-induced apoptosis through the p75 TNF receptor.
Probab=46.81 E-value=19 Score=20.83 Aligned_cols=16 Identities=31% Similarity=0.445 Sum_probs=13.4
Q ss_pred cEEEecCCEEEEEEEe
Q psy88 4 PKNVCEGDRVVVDVRN 19 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N 19 (75)
.+++++||+|.|++.+
T Consensus 92 vf~L~~gD~L~v~v~~ 107 (125)
T smart00207 92 LFPLTAGDRLSVNVTE 107 (125)
T ss_pred EEEecCCCEEEEEeCC
Confidence 5688999999998764
No 126
>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=45.82 E-value=16 Score=20.87 Aligned_cols=16 Identities=38% Similarity=0.995 Sum_probs=13.3
Q ss_pred cccccCCCCEEEEEEc
Q psy88 48 TQCPITQGNTFRYQFT 63 (75)
Q Consensus 48 ~~~~i~pG~~~~y~~~ 63 (75)
..||+.+|+.++|.+.
T Consensus 84 ~~CPi~~G~~~~~~~~ 99 (134)
T PF02221_consen 84 LSCPIKAGEYYTYTYT 99 (134)
T ss_dssp TTSTBTTTEEEEEEEE
T ss_pred ccCccCCCcEEEEEEE
Confidence 3799999998887776
No 127
>cd08068 MPN_BRCC36 Mov34/MPN/PAD-1 family: BRCC36, a subunit of BRCA1-A complex. BRCC36 (BRCA1-A complex subunit BRCC36; BRCA1/BRCA2-containing complex subunit 36; BRCA1/BRCA2-containing complex subunit 3; BRCC3; BRISC complex subunit BRCC36; BRCC36 isopeptidase complex; Lys-63-specific deubiquitinase BRCC36) and BRCC36-like domains are members of JAMM/MPN+ deubiquitinases (DUBs), possibly with Zn2+-dependent ubiquitin isopeptidase activity. BRCC36 is part of the BRCA1/BRCA2/BARD1-containing nuclear complex that displays an E3 ubiquitin ligase activity. It is targeted to DNA damage foci after irradiation; RAP80 recruits the Abraxas-BRCC36-BRCA1-BARD1 complex to DNA double strand breaks (DSBs) for DNA repair through specific recognition of Lys 63-linked polyubiquitinated proteins by its tandem ubiquitin-interacting motifs. A new protein, MERIT40 (mediator of RAP80 interactions and targeting 40 kDa), also named NBA1 (new component of the BRCA1 A complex), exists in the same BRCA1-contai
Probab=45.13 E-value=10 Score=25.05 Aligned_cols=8 Identities=25% Similarity=0.812 Sum_probs=6.1
Q ss_pred eeEEccCC
Q psy88 68 THFWHAHT 75 (75)
Q Consensus 68 t~~YH~H~ 75 (75)
.=|||||.
T Consensus 92 VGwYHSHP 99 (244)
T cd08068 92 VGWYHSHP 99 (244)
T ss_pred EEEEecCC
Confidence 34999994
No 128
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=44.78 E-value=26 Score=19.25 Aligned_cols=17 Identities=29% Similarity=0.268 Sum_probs=14.1
Q ss_pred cEEEecCCEEEEEEEeC
Q psy88 4 PKNVCEGDRVVVDVRNS 20 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~ 20 (75)
.|++++||.|.|.+...
T Consensus 41 ~iwI~~GD~VlVe~~~~ 57 (83)
T smart00652 41 KVWIRRGDIVLVDPWDF 57 (83)
T ss_pred cEEEcCCCEEEEEecCC
Confidence 58899999999987643
No 129
>COG4895 Uncharacterized conserved protein [Function unknown]
Probab=44.23 E-value=28 Score=17.99 Aligned_cols=37 Identities=24% Similarity=0.247 Sum_probs=24.5
Q ss_pred EecCCEEEEEEEeCCCC------------CCceEEeCCccccCCCCCCCCCc
Q psy88 7 VCEGDRVVVDVRNSMDG------------LENTIHWHGIHQRGTQYSDGVPF 46 (75)
Q Consensus 7 ~~~Gd~v~i~~~N~~~~------------~~~~iH~HG~~~~~~~~~DG~~~ 46 (75)
+++|-+|.|.++-.-.. ...+.|.||+.... .||.-+
T Consensus 9 I~~GL~VdIVlKqDQkTGKlTrGvVk~iLT~S~~HPHGIKVrL---~dGqvG 57 (63)
T COG4895 9 IRPGLTVDIVLKQDQKTGKLTRGVVKAILTRSPSHPHGIKVRL---TDGQVG 57 (63)
T ss_pred cCCCcEEEEEEeccccCCcchhHHHHHHHhCCCCCCCceEEEe---ecCccc
Confidence 46788888887754321 13578999998764 477544
No 130
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=44.05 E-value=26 Score=20.02 Aligned_cols=16 Identities=31% Similarity=0.341 Sum_probs=13.4
Q ss_pred cEEEecCCEEEEEEEe
Q psy88 4 PKNVCEGDRVVVDVRN 19 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N 19 (75)
.|++++||.|.|.+.-
T Consensus 57 ~IwI~~GD~VlVe~~~ 72 (100)
T PRK04012 57 RMWIREGDVVIVAPWD 72 (100)
T ss_pred cEEecCCCEEEEEecc
Confidence 6899999999998643
No 131
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=43.69 E-value=14 Score=21.72 Aligned_cols=17 Identities=41% Similarity=0.593 Sum_probs=12.8
Q ss_pred cEEEecCCEEEEEEEeC
Q psy88 4 PKNVCEGDRVVVDVRNS 20 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~ 20 (75)
++.++.||.|+|.+...
T Consensus 49 ~~~~~~GD~V~v~i~~~ 65 (135)
T PF04246_consen 49 PIGAKVGDRVEVEIPES 65 (135)
T ss_pred CCCCCCCCEEEEEeccc
Confidence 45678899988887654
No 132
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=43.60 E-value=16 Score=20.54 Aligned_cols=15 Identities=20% Similarity=0.113 Sum_probs=11.8
Q ss_pred cEEEecCCEEEEEEE
Q psy88 4 PKNVCEGDRVVVDVR 18 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~ 18 (75)
-+.++.||.|+|.=.
T Consensus 53 ~~~~k~GD~V~I~Et 67 (87)
T COG0186 53 CNEAKVGDIVRIAET 67 (87)
T ss_pred cccCCCCCEEEEEEc
Confidence 467899999999644
No 133
>TIGR03396 PC_PLC phospholipase C, phosphocholine-specific, Pseudomonas-type. Members of this protein family are bacterial, phosphatidylcholine-hydrolyzing phospholipase C enzymes, with a characteristic domain architecture as found in hemolytyic (PlcH) and nonhemolytic (PlcN) secreted enzymes of Pseudomonas aeruginosa. PlcH hydrolyzes phosphatidylcholine to diacylglycerol and phosphocholine, but unlike PlcN can also hydrolyze sphingomyelin to ceramide ((N-acylsphingosine)) and phosphocholine. Members of this family share the twin-arginine signal sequence for Sec-independent transport across the plasma membrane. PlcH is secreted as a heterodimer with a small chaperone, PlcR, encoded immediately downstream.
Probab=42.34 E-value=1.6e+02 Score=22.66 Aligned_cols=46 Identities=11% Similarity=0.190 Sum_probs=28.9
Q ss_pred CCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc
Q psy88 10 GDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT 63 (75)
Q Consensus 10 Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~ 63 (75)
...|+|+|.|... ....++.---. ..++.+. ..-|++|++.+..|.
T Consensus 604 ~G~L~L~L~N~G~-~a~~ftV~d~~-----Y~~~~pr--~ytV~aG~~~~~~w~ 649 (690)
T TIGR03396 604 NGNLYLTLSNAGR-SPVTVTVTDNA-----YGGAGPR--TVTVAPGQRVELHWD 649 (690)
T ss_pred CCEEEEEEEeCCC-CcEEEEEEeCC-----CCCCCCE--EEEECCCCEEEEEEe
Confidence 4469999999987 66666653211 1122231 234788999888887
No 134
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=41.82 E-value=17 Score=18.85 Aligned_cols=15 Identities=27% Similarity=0.257 Sum_probs=9.9
Q ss_pred cEEEecCCEEEEEEE
Q psy88 4 PKNVCEGDRVVVDVR 18 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~ 18 (75)
.|++++||.|.|.+.
T Consensus 39 ~iwI~~GD~V~V~~~ 53 (65)
T PF01176_consen 39 RIWIKRGDFVLVEPS 53 (65)
T ss_dssp CC---TTEEEEEEES
T ss_pred eEecCCCCEEEEEec
Confidence 578899999999874
No 135
>PF14796 AP3B1_C: Clathrin-adaptor complex-3 beta-1 subunit C-terminal
Probab=41.72 E-value=82 Score=19.24 Aligned_cols=47 Identities=13% Similarity=0.155 Sum_probs=25.8
Q ss_pred EEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcc---cccccCCCCEEEEEEc
Q psy88 12 RVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFV---TQCPITQGNTFRYQFT 63 (75)
Q Consensus 12 ~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~---~~~~i~pG~~~~y~~~ 63 (75)
.|+++|.|..+..-..||.-.-.. .+|.... .-.-++||++.+..+-
T Consensus 88 sIql~ftN~s~~~i~~I~i~~k~l-----~~g~~i~~F~~I~~L~pg~s~t~~lg 137 (145)
T PF14796_consen 88 SIQLTFTNNSDEPIKNIHIGEKKL-----PAGMRIHEFPEIESLEPGASVTVSLG 137 (145)
T ss_pred EEEEEEEecCCCeecceEECCCCC-----CCCcEeeccCcccccCCCCeEEEEEE
Confidence 478999999884444555422111 2232110 1123789999886653
No 136
>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=41.28 E-value=25 Score=18.68 Aligned_cols=20 Identities=20% Similarity=0.370 Sum_probs=14.4
Q ss_pred ccCCCCEEEEEEc---CCCeeeE
Q psy88 51 PITQGNTFRYQFT---ANAGTHF 70 (75)
Q Consensus 51 ~i~pG~~~~y~~~---~~~Gt~~ 70 (75)
.++||++.++.|. ..+|.+-
T Consensus 56 ~L~~g~~~~v~~~~~~~~~G~~~ 78 (101)
T PF07705_consen 56 SLAPGESETVTFTWTPPSPGSYT 78 (101)
T ss_dssp EB-TTEEEEEEEEEE-SS-CEEE
T ss_pred CcCCCcEEEEEEEEEeCCCCeEE
Confidence 5789999999988 5677664
No 137
>PF08234 Spindle_Spc25: Chromosome segregation protein Spc25; InterPro: IPR013255 This is a family of chromosome segregation proteins. It contains Spc25, which is a conserved eukaryotic kinetochore protein involved in cell division. In fungi the Spc25 protein is a subunit of the Nuf2-Ndc80 complex [], and in vertebrates it forms part of the Ndc80 complex []. ; PDB: 2VE7_B.
Probab=41.25 E-value=27 Score=18.53 Aligned_cols=18 Identities=17% Similarity=0.100 Sum_probs=10.9
Q ss_pred EEEecCCEEEEEEEeCCC
Q psy88 5 KNVCEGDRVVVDVRNSMD 22 (75)
Q Consensus 5 i~~~~Gd~v~i~~~N~~~ 22 (75)
|++..+|.+++.|.|-.+
T Consensus 1 ie~~~~d~lkf~F~~id~ 18 (74)
T PF08234_consen 1 IEAIGGDQLKFVFTNIDP 18 (74)
T ss_dssp EE--STT-EEEEE-S-BT
T ss_pred CcccCCceEEEEEeEcCC
Confidence 677889999999998754
No 138
>cd00175 SNc Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds.
Probab=41.19 E-value=27 Score=19.85 Aligned_cols=65 Identities=18% Similarity=0.226 Sum_probs=36.9
Q ss_pred EEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCC----CC--CCccc-----ccccCCCCEEEEEEc--CCCeeeEEc
Q psy88 6 NVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYS----DG--VPFVT-----QCPITQGNTFRYQFT--ANAGTHFWH 72 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~----DG--~~~~~-----~~~i~pG~~~~y~~~--~~~Gt~~YH 72 (75)
||--||+++|...+. ....+-+-|+..+..... ++ .+... ......|...++.+. +..|.+.-+
T Consensus 1 rV~dGDt~~v~~~~~---~~~~vrL~gId~Pe~~~~~~~~~~~~~~~g~~A~~~l~~~l~~~~V~i~~~~~d~~gr~la~ 77 (129)
T cd00175 1 RVIDGDTIRVRLPPG---PLITVRLSGIDAPETARPNKGKSETDEPFGEEAKEFLKKLLLGKKVQVEVDSKDRYGRTLGT 77 (129)
T ss_pred CeecCcEEEEEeCCC---CEEEEEEEeecCccccCCccCCCCCCCchHHHHHHHHHHHhCCCEEEEEEccCCCCCCEEEE
Confidence 466799999876655 356888899887643211 11 11100 001235677777666 566665544
Q ss_pred c
Q psy88 73 A 73 (75)
Q Consensus 73 ~ 73 (75)
|
T Consensus 78 v 78 (129)
T cd00175 78 V 78 (129)
T ss_pred E
Confidence 3
No 139
>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=40.80 E-value=26 Score=19.79 Aligned_cols=15 Identities=40% Similarity=0.946 Sum_probs=13.1
Q ss_pred ccccCCCCEEEEEEc
Q psy88 49 QCPITQGNTFRYQFT 63 (75)
Q Consensus 49 ~~~i~pG~~~~y~~~ 63 (75)
.||+.+|+.++|...
T Consensus 71 ~CPl~~G~~~~~~~~ 85 (118)
T smart00737 71 KCPIEKGETVNYTNS 85 (118)
T ss_pred CCCCCCCeeEEEEEe
Confidence 699999999888765
No 140
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=40.78 E-value=41 Score=15.93 Aligned_cols=16 Identities=31% Similarity=0.177 Sum_probs=13.2
Q ss_pred EEecCCEEEEEEEeCC
Q psy88 6 NVCEGDRVVVDVRNSM 21 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~~ 21 (75)
.++.||.|++.+....
T Consensus 41 ~~~~G~~v~~~v~~~d 56 (65)
T cd00164 41 VFKVGDEVEVKVLEVD 56 (65)
T ss_pred EeCCCCEEEEEEEEEc
Confidence 5789999999998653
No 141
>PF02563 Poly_export: Polysaccharide biosynthesis/export protein; InterPro: IPR003715 The extracellular polysaccharide colanic acid (CA) is produced by species of the family Enterobacteriaceae. In Escherichia coli (strain K12) the CA cluster comprises 19 genes. The wzx gene encodes a protein with multiple transmembrane segments that may function in export of the CA repeat unit from the cytoplasm into the periplasm in a process analogous to O-unit export. The CA gene clusters may be involved in the export of polysaccharide from the cell [].; GO: 0015159 polysaccharide transmembrane transporter activity, 0015774 polysaccharide transport, 0016020 membrane; PDB: 2W8I_E 2W8H_E 2J58_D.
Probab=40.35 E-value=25 Score=18.83 Aligned_cols=20 Identities=15% Similarity=0.072 Sum_probs=10.3
Q ss_pred ccEEEecCCEEEEEEEeCCC
Q psy88 3 YPKNVCEGDRVVVDVRNSMD 22 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N~~~ 22 (75)
...++..||.++|.+.+..+
T Consensus 9 ~~y~l~pGD~l~i~v~~~~~ 28 (82)
T PF02563_consen 9 PEYRLGPGDVLRISVFGWPE 28 (82)
T ss_dssp ------TT-EEEEEETT-HH
T ss_pred CCCEECCCCEEEEEEecCCC
Confidence 34678999999999987643
No 142
>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=39.93 E-value=17 Score=20.25 Aligned_cols=14 Identities=21% Similarity=0.444 Sum_probs=9.4
Q ss_pred cccCCCCEEEEEEc
Q psy88 50 CPITQGNTFRYQFT 63 (75)
Q Consensus 50 ~~i~pG~~~~y~~~ 63 (75)
-.+.||++|.|.=-
T Consensus 57 P~L~pGe~f~Y~S~ 70 (90)
T PF04379_consen 57 PVLAPGESFEYTSG 70 (90)
T ss_dssp -EE-TTEEEEEEEE
T ss_pred ceECCCCcEEEcCC
Confidence 34689999999744
No 143
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=39.57 E-value=21 Score=17.08 Aligned_cols=15 Identities=27% Similarity=0.503 Sum_probs=11.7
Q ss_pred EEecCCEEEEEEEeC
Q psy88 6 NVCEGDRVVVDVRNS 20 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~ 20 (75)
.+++||.|.|...+.
T Consensus 20 ~l~~Gd~v~i~~~~~ 34 (47)
T PF04014_consen 20 GLKPGDEVEIEVEGD 34 (47)
T ss_dssp TSSTTTEEEEEEETT
T ss_pred CCCCCCEEEEEEeCC
Confidence 357899999988764
No 144
>PF08496 Peptidase_S49_N: Peptidase family S49 N-terminal; InterPro: IPR013703 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 is found to the N terminus of bacterial signal peptidases that belong to the MEROPS peptidase family S49 (protease IV family, clan SK) (see also IPR002142 from INTERPRO) [, ]. ; GO: 0004252 serine-type endopeptidase activity, 0005886 plasma membrane
Probab=39.08 E-value=35 Score=20.98 Aligned_cols=24 Identities=21% Similarity=0.297 Sum_probs=18.3
Q ss_pred EEecCCEEEEEEEeCCCCCCceEEeCCc
Q psy88 6 NVCEGDRVVVDVRNSMDGLENTIHWHGI 33 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~~~~~~~~iH~HG~ 33 (75)
.+++||+|.|++..... .+|-.|+
T Consensus 127 ~a~~~DeV~~rLES~GG----~Vh~YGL 150 (155)
T PF08496_consen 127 VATPEDEVLVRLESPGG----MVHGYGL 150 (155)
T ss_pred hCCCCCeEEEEEecCCc----eeeccch
Confidence 46889999999988755 5565665
No 145
>KOG1555|consensus
Probab=39.05 E-value=12 Score=25.75 Aligned_cols=8 Identities=25% Similarity=0.812 Sum_probs=6.0
Q ss_pred eeEEccCC
Q psy88 68 THFWHAHT 75 (75)
Q Consensus 68 t~~YH~H~ 75 (75)
.=|||||.
T Consensus 118 VGWYHSHP 125 (316)
T KOG1555|consen 118 VGWYHSHP 125 (316)
T ss_pred EeeccCCC
Confidence 34999993
No 146
>cd04980 IgV_L_kappa Immunoglobulin (Ig) light chain, kappa type, variable (V) domain. IgV_L_kappa: Immunoglobulin (Ig) light chain, kappa type, variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determine the type of immunoglobulin: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains.
Probab=39.01 E-value=67 Score=17.50 Aligned_cols=29 Identities=17% Similarity=0.314 Sum_probs=19.7
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEe
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHW 30 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~ 30 (75)
+..+.+++|+.|.++=.-........++|
T Consensus 7 p~~~~v~~G~~v~L~C~~~~~~~~~~~~W 35 (106)
T cd04980 7 PATLSVSPGESATISCKASQSVSSNYLAW 35 (106)
T ss_pred CCcEEECCCCCEEEEEEECCCCCCCcEEE
Confidence 34678999999999876432202456887
No 147
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=38.95 E-value=28 Score=18.25 Aligned_cols=17 Identities=24% Similarity=0.362 Sum_probs=12.0
Q ss_pred EEecCCEEEEEEEeCCC
Q psy88 6 NVCEGDRVVVDVRNSMD 22 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~~~ 22 (75)
.++.||.|.+.|.-..+
T Consensus 42 ~l~~Gd~V~F~~~~~~~ 58 (70)
T PF11604_consen 42 GLKPGDKVRFTFERTDD 58 (70)
T ss_dssp S-STT-EEEEEEEEETT
T ss_pred cCCCCCEEEEEEEECCC
Confidence 36789999999987654
No 148
>MTH00038 COX2 cytochrome c oxidase subunit II; Provisional
Probab=38.87 E-value=1.1e+02 Score=19.87 Aligned_cols=55 Identities=15% Similarity=0.097 Sum_probs=33.9
Q ss_pred cEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEcc
Q psy88 4 PKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHA 73 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~ 73 (75)
.+.+-.|..+++.++-..- | |+...+.. |.- . -.-||..-...+. +++|+|.--|
T Consensus 141 ~lvlP~~~~v~~~~tS~DV-----i--Hsf~iP~l----g~k---~-daiPG~~~~~~~~~~~~G~~~g~C 196 (229)
T MTH00038 141 RLVLPYQTPIRVLVSSADV-----L--HSWAVPSL----GVK---M-DAVPGRLNQTTFFISRTGLFYGQC 196 (229)
T ss_pred eEEEecCeEEEEEEEECCc-----c--cccccccc----Cce---e-ecCCCceEEEEEEcCCCEEEEEEc
Confidence 4566677777777665531 2 44433321 111 1 1448888888888 9999998777
No 149
>cd04983 IgV_TCR_alpha_like Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar proteins. IgV_TCR_alpha: immunoglobulin (Ig) variable domain of the alpha chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta, polypeptide chains with variable (V) and constant (C) regions. This group represents the variable domain of the alpha chain of TCRs and also includes the variable domain of delta chains of TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The variable domain of TCRs is responsible for antigen recognition, and is located at the N-terminus of the receptor. Gamma/delta TCRs recognize intact protein antigens; they recognize proteins antigens directly and without antigen processing, and MHC independently of the bound peptide.
Probab=38.65 E-value=67 Score=17.36 Aligned_cols=28 Identities=21% Similarity=0.313 Sum_probs=21.0
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEe
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHW 30 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~ 30 (75)
+..+.+.+|+.|.|.=.=... ....++|
T Consensus 5 ~~~v~~~~G~~v~L~C~~~~~-~~~~v~W 32 (109)
T cd04983 5 PQSLSVQEGENVTLNCNYSTS-TFYYLFW 32 (109)
T ss_pred CCceEEcCCCCEEEEEEECCC-CccEEEE
Confidence 457889999999998764443 4668888
No 150
>cd05720 Ig_CD8_alpha Immunoglobulin (Ig) like domain of CD8 alpha chain. Ig_CD8_alpha: immunoglobulin (Ig)-like domain in CD8 alpha. The CD8 glycoprotein plays an essential role in the control of T-cell selection, maturation and the T-cell receptor (TCR)-mediated response to peptide antigen. CD8 is comprised of alpha and beta subunits and is expressed as either an alphaalpha or alphabeta dimer. Both dimeric isoforms can serve as a coreceptor for T cell activation and differentiation, however they have distinct physiological roles, different cellular distributions, unique binding partners etc. Each CD8 subunit is comprised of an extracellular domain containing a v-type Ig-like domain, a single pass transmembrane portion and a short intracellular domain. The Ig domain of CD8 alpha binds to antibodies.
Probab=38.49 E-value=59 Score=17.92 Aligned_cols=24 Identities=13% Similarity=0.205 Sum_probs=15.8
Q ss_pred EEecCCEEEEEEEeCCCCCCceEEe
Q psy88 6 NVCEGDRVVVDVRNSMDGLENTIHW 30 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~~~~~~~~iH~ 30 (75)
.+++|+.|+|.=.-... ....++|
T Consensus 2 ~v~~G~~vtL~C~~~~~-~~~~v~W 25 (104)
T cd05720 2 DAELGQKVELKCEVLNS-SPTGCSW 25 (104)
T ss_pred cccCCCeEEEEEEecCC-CCCcEEE
Confidence 36889999997654332 3456777
No 151
>cd08961 GH64-TLP-SF glycoside hydrolase family 64 (beta-1,3-glucanases which produce specific pentasaccharide oligomers) and thaumatin-like proteins. This superfamily includes glycoside hydrolases of family 64 (GH64), these are mostly bacterial beta-1,3-glucanases which cleave long-chain polysaccharide beta-1,3-glucans, into specific pentasaccharide oligomers and are implicated in fungal cell wall degradation. Also included in this superfamily are thaumatin, the sweet-tasting protein from the African berry Thaumatococcus daniellii, and thaumatin-like proteins (TLPs) which are involved in host defense and a wide range of developmental processes in fungi, plants, and animals. Like GH64s, some TLPs also hydrolyze the beta-1,3-glucans of the type commonly found in fungal walls. Plant TLPs are classified as pathogenesis-related (PR) protein family 5 (PR5), their expression is induced by environmental stresses such as pathogen/pest attack, drought and cold. Several members of the plant TLP
Probab=38.48 E-value=95 Score=19.05 Aligned_cols=21 Identities=14% Similarity=0.328 Sum_probs=16.7
Q ss_pred ccCCCCEEEEEEc-CCCeeeEE
Q psy88 51 PITQGNTFRYQFT-ANAGTHFW 71 (75)
Q Consensus 51 ~i~pG~~~~y~~~-~~~Gt~~Y 71 (75)
.+.||+++++.++ .-.|..|.
T Consensus 30 ~L~pG~s~si~vP~~wsGRIW~ 51 (153)
T cd08961 30 GLAPGRSTTIQIPKGFSGRIWF 51 (153)
T ss_pred ccCCCCcEEEEecCCceEEEEE
Confidence 4789999999988 66677774
No 152
>cd05737 Ig_Myomesin_like_C C-temrinal immunoglobulin (Ig)-like domain of myomesin and M-protein. Ig_Myomesin_like_C: domain similar to the C-temrinal immunoglobulin (Ig)-like domain of myomesin and M-protein. Myomesin and M-protein are both structural proteins localized to the M-band, a transverse structure in the center of the sarcomere, and are candidates for M-band bridges. Both proteins are modular, consisting mainly of repetitive Ig-like and fibronectin type III (FnIII) domains. Myomesin is expressed in all types of vertebrate striated muscle; M-protein has a muscle-type specific expression pattern. Myomesin is present in both slow and fast fibers; M-protein is present only in fast fibers. It has been suggested that myomesin acts as a molecular spring with alternative splicing as a means of modifying its elasticity.
Probab=38.10 E-value=65 Score=17.08 Aligned_cols=28 Identities=14% Similarity=0.222 Sum_probs=19.2
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEe
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHW 30 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~ 30 (75)
+..+.+++|+.+++.-.=... ..-.+.|
T Consensus 8 p~~v~v~~G~~v~L~C~v~G~-P~p~v~W 35 (92)
T cd05737 8 PDVVTIMEGKTLNLTCTVFGD-PDPEVSW 35 (92)
T ss_pred CceEEEeCCCcEEEEEEEEec-CCCeEEE
Confidence 345789999999988764433 2336777
No 153
>PF01954 DUF104: Protein of unknown function DUF104; InterPro: IPR008203 This family includes short archaebacterial proteins of unknown function. Archaeoglobus fulgidus has twelve copies of this protein, with several being clustered together in the genome.; PDB: 2NWT_A.
Probab=37.95 E-value=21 Score=18.50 Aligned_cols=19 Identities=26% Similarity=0.541 Sum_probs=9.6
Q ss_pred cccEEEecCCEEEEEEEeC
Q psy88 2 LYPKNVCEGDRVVVDVRNS 20 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~ 20 (75)
+-++.+.+|+.|+|.+...
T Consensus 17 l~~~~L~Eg~~V~i~I~~~ 35 (60)
T PF01954_consen 17 LEPVDLPEGEEVKITIEEE 35 (60)
T ss_dssp CS-----TTEEEEEEE---
T ss_pred CCCCCCCCCCEEEEEEecc
Confidence 4567789999999999875
No 154
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=37.83 E-value=53 Score=18.01 Aligned_cols=18 Identities=6% Similarity=0.032 Sum_probs=14.9
Q ss_pred cEEEecCCEEEEEEEeCC
Q psy88 4 PKNVCEGDRVVVDVRNSM 21 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~ 21 (75)
.+.++.||.||+++....
T Consensus 53 ~~~i~~g~~VR~rV~~v~ 70 (88)
T cd04462 53 DIVIKKDTEVRLKIIGTR 70 (88)
T ss_pred cEEECCCCEEEEEEEEEE
Confidence 467899999999987653
No 155
>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=37.81 E-value=15 Score=22.35 Aligned_cols=18 Identities=28% Similarity=0.516 Sum_probs=10.3
Q ss_pred CcccEEEecCCEEEEEEE
Q psy88 1 MLYPKNVCEGDRVVVDVR 18 (75)
Q Consensus 1 ~~~~i~~~~Gd~v~i~~~ 18 (75)
|+.+=++.+|++|+|++.
T Consensus 38 mPVpk~I~~GeTvEIR~~ 55 (137)
T PF12988_consen 38 MPVPKKIKKGETVEIRCE 55 (137)
T ss_dssp ----SS--TTEEEEEEEE
T ss_pred eccccccCCCCEEEEEEE
Confidence 445557789999999876
No 156
>PF14250 AbrB-like: AbrB-like transcriptional regulator
Probab=37.58 E-value=19 Score=19.47 Aligned_cols=15 Identities=13% Similarity=0.271 Sum_probs=11.5
Q ss_pred EEEecCCEEEEEEEe
Q psy88 5 KNVCEGDRVVVDVRN 19 (75)
Q Consensus 5 i~~~~Gd~v~i~~~N 19 (75)
+.++.||+++|.+--
T Consensus 51 m~L~PGdEFeI~Lgr 65 (71)
T PF14250_consen 51 MGLKPGDEFEIKLGR 65 (71)
T ss_pred hCCCCCCEEEEEeCc
Confidence 457899999998643
No 157
>PF00229 TNF: TNF(Tumour Necrosis Factor) family ; InterPro: IPR006052 Cytokines can be grouped into a family on the basis of sequence, functional and structural similarities [, , ]. Tumor necrosis factor (TNF) (also known as TNF-alpha or cachectin) is a monocyte-derived cytotoxin that has been implicated in tumour regression, septic shock and cachexia [, ]. The protein is synthesised as a prohormone with an unusually long and atypical signal sequence, which is absent from the mature secreted cytokine []. A short hydrophobic stretch of amino acids serves to anchor the prohormone in lipid bilayers []. Both the mature protein and a partially-processed form of the hormone are secreted after cleavage of the propeptide []. There are a number of different families of TNF, but all these cytokines seem to form homotrimeric (or heterotrimeric in the case of LT-alpha/beta) complexes that are recognised by their specific receptors. The following cytokines can be grouped into a family on the basis of sequence, functional, and structural similarities [, , ]: Tumor Necrosis Factor (TNF) (also known as cachectin or TNF-alpha) [, ] is a cytokine which has a wide variety of functions. It can cause cytolysis of certain tumor cell lines; it is involved in the induction of cachexia; it is a potent pyrogen, causing fever by direct action or by stimulation of interleukin-1 secretion; finally, it can stimulate cell proliferation and induce cell differentiation under certain conditions. Lymphotoxin-alpha (LT-alpha) and lymphotoxin-beta (LT-beta), two related cytokines produced by lymphocytes and which are cytotoxic for a wide range of tumor cells in vitro and in vivo []. T cell antigen gp39 (CD40L), a cytokine which seems to be important in B-cell development and activation. CD27L, a cytokine which plays a role in T-cell activation. It induces the proliferation of costimulated T cells and enhances the generation of cytolytic T cells. CD30L, a cytokine which induces proliferation of T cells. FASL, a cytokine involved in cell death []. 4-1BBL, a inducible T cell surface molecule that contributes to T-cell stimulation. OX40L, a cytokine that co-stimulates T cell proliferation and cytokine production []. TNF-related apoptosis inducing ligand (TRAIL), a cytokine that induces apoptosis []. TNF-alpha is synthesised as a type II membrane protein which then undergoes post-translational cleavage liberating the extracellular domain. CD27L, CD30L, CD40L, FASL, LT-beta, 4-1BBL and TRAIL also appear to be type II membrane proteins. LT-alpha is a secreted protein. All these cytokines seem to form homotrimeric (or heterotrimeric in the case of LT-alpha/beta) complexes that are recognised by their specific receptors. The PROSITE pattern for this family is located in a beta-strand in the central section of the protein which is conserved across all members.; GO: 0005164 tumor necrosis factor receptor binding, 0006955 immune response, 0016020 membrane; PDB: 3QBQ_C 1IQA_B 1S55_C 1JTZ_Z 3ME2_A 3QD6_C 3LKJ_B 1I9R_A 1ALY_A 2X29_A ....
Probab=37.34 E-value=22 Score=20.35 Aligned_cols=15 Identities=33% Similarity=0.415 Sum_probs=12.7
Q ss_pred cEEEecCCEEEEEEE
Q psy88 4 PKNVCEGDRVVVDVR 18 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~ 18 (75)
.+++++||+|.|++.
T Consensus 93 v~~L~~gd~l~v~v~ 107 (127)
T PF00229_consen 93 VFHLQAGDRLSVRVS 107 (127)
T ss_dssp EEEECTTEEEEEEES
T ss_pred eEEcCCCCEEEEEEC
Confidence 468999999999965
No 158
>PF03658 Ub-RnfH: RnfH family Ubiquitin; InterPro: IPR005346 This is a small family of proteins of unknown function.; PDB: 2HJ1_B.
Probab=37.13 E-value=22 Score=19.78 Aligned_cols=11 Identities=36% Similarity=0.543 Sum_probs=6.7
Q ss_pred EEecCCEEEEE
Q psy88 6 NVCEGDRVVVD 16 (75)
Q Consensus 6 ~~~~Gd~v~i~ 16 (75)
.+++||+|+|.
T Consensus 61 ~L~~GDRVEIY 71 (84)
T PF03658_consen 61 VLRDGDRVEIY 71 (84)
T ss_dssp B--TT-EEEEE
T ss_pred cCCCCCEEEEe
Confidence 46899999985
No 159
>cd03696 selB_II selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.
Probab=36.40 E-value=36 Score=18.03 Aligned_cols=15 Identities=27% Similarity=0.505 Sum_probs=12.1
Q ss_pred EEecCCEEEEEEEeC
Q psy88 6 NVCEGDRVVVDVRNS 20 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~ 20 (75)
.+..||.+.|.+.|.
T Consensus 56 ~a~aGd~v~i~l~~~ 70 (83)
T cd03696 56 EAKAGDRVALNLTGV 70 (83)
T ss_pred EEcCCCEEEEEEcCC
Confidence 477899999998764
No 160
>COG5004 P2-like prophage tail protein X [General function prediction only]
Probab=36.31 E-value=13 Score=19.81 Aligned_cols=14 Identities=29% Similarity=0.228 Sum_probs=10.1
Q ss_pred CcccEEEecCCEEE
Q psy88 1 MLYPKNVCEGDRVV 14 (75)
Q Consensus 1 ~~~~i~~~~Gd~v~ 14 (75)
|++..|..+||+|.
T Consensus 1 ~~~~~Rt~~gDtvD 14 (70)
T COG5004 1 SLMIVRTRQGDTVD 14 (70)
T ss_pred CceEEEeccCchHH
Confidence 56777888888753
No 161
>TIGR03635 S17_bact 30S ribosomal protein S17. This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17.
Probab=36.23 E-value=23 Score=18.90 Aligned_cols=11 Identities=27% Similarity=0.190 Sum_probs=9.3
Q ss_pred EEecCCEEEEE
Q psy88 6 NVCEGDRVVVD 16 (75)
Q Consensus 6 ~~~~Gd~v~i~ 16 (75)
.+++||.|+|.
T Consensus 48 ~~k~GD~V~I~ 58 (71)
T TIGR03635 48 ECKVGDVVRII 58 (71)
T ss_pred CCCCCCEEEEE
Confidence 47899999986
No 162
>PF04151 PPC: Bacterial pre-peptidase C-terminal domain; InterPro: IPR007280 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. This domain is normally found at the C terminus of secreted archaeal and bacterial peptidases, the majority of which belong to MEROPS peptidase families M4 (vibriolysin, IPR001570 from INTERPRO), M9A amd M9B (microbial collangenase, IPR002169 from INTERPRO), M28 (aminopeptidase Ap1, IPR007484 from INTERPRO) and S8 (subtilisin family peptidases, IPR000209 from INTERPRO).; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 4DY5_B 4DXZ_A 4DY3_B 3JQW_A 3JQX_C 1NQJ_B 1NQD_A 2O8O_A 1WMF_A 1WME_A ....
Probab=36.10 E-value=64 Score=16.39 Aligned_cols=18 Identities=17% Similarity=0.279 Sum_probs=15.8
Q ss_pred cEEEecCCEEEEEEEeCC
Q psy88 4 PKNVCEGDRVVVDVRNSM 21 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~ 21 (75)
.+.+++|++++|.+.+..
T Consensus 6 ~f~v~ag~~l~i~l~~~~ 23 (70)
T PF04151_consen 6 SFTVPAGGTLTIDLSGGS 23 (70)
T ss_dssp EEEESTTEEEEEEECETT
T ss_pred EEEEcCCCEEEEEEcCCC
Confidence 578999999999998876
No 163
>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=36.04 E-value=56 Score=18.91 Aligned_cols=16 Identities=19% Similarity=0.202 Sum_probs=13.6
Q ss_pred ccEEEecCCEEEEEEE
Q psy88 3 YPKNVCEGDRVVVDVR 18 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~ 18 (75)
..|.+++|+.+.|.+.
T Consensus 25 ~~LVVRRGQ~F~i~l~ 40 (118)
T PF00868_consen 25 PRLVVRRGQPFTITLR 40 (118)
T ss_dssp SSEEEETTSEEEEEEE
T ss_pred CCEEEECCCEEEEEEE
Confidence 3588999999998887
No 164
>PF07679 I-set: Immunoglobulin I-set domain; InterPro: IPR013098 The basic structure of immunoglobulin (Ig) molecules is a tetramer of two light chains and two heavy chains linked by disulphide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains: alpha, delta, epsilon, gamma and mu, all consisting of a variable domain (VH) and three (in alpha, delta and gamma) or four (in epsilon and mu) constant domains (CH1 to CH4). Ig molecules are highly modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. The domains in Ig and Ig-like molecules are grouped into four types: V-set (variable; IPR013106 from INTERPRO), C1-set (constant-1; IPR003597 from INTERPRO), C2-set (constant-2; IPR008424 from INTERPRO) and I-set (intermediate; IPR013098 from INTERPRO) []. Structural studies have shown that these domains share a common core Greek-key beta-sandwich structure, with the types differing in the number of strands in the beta-sheets as well as in their sequence patterns [, ]. Immunoglobulin-like domains that are related in both sequence and structure can be found in several diverse protein families. Ig-like domains are involved in a variety of functions, including cell-cell recognition, cell-surface receptors, muscle structure and the immune system []. This entry represents I-set domains, which are found in several cell adhesion molecules, including vascular (VCAM), intercellular (ICAM), neural (NCAM) and mucosal addressin (MADCAM) cell adhesion molecules, as well as junction adhesion molecules (JAM). I-set domains are also present in several other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1 [], and the signalling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis [].; PDB: 3MTR_A 2EDK_A 3DMK_B 1KOA_A 3NCM_A 2NCM_A 2V9Q_A 2CR3_A 3QQN_A 3QR2_A ....
Probab=35.80 E-value=67 Score=16.51 Aligned_cols=28 Identities=25% Similarity=0.356 Sum_probs=19.1
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEe
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHW 30 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~ 30 (75)
+..+.+++|+.+.+...=... ....+.|
T Consensus 7 ~~~~~v~~G~~~~l~c~~~~~-p~~~v~W 34 (90)
T PF07679_consen 7 PKDVTVKEGESVTLECEVSGN-PPPTVTW 34 (90)
T ss_dssp SSEEEEETTSEEEEEEEEEES-SSSEEEE
T ss_pred cCCEEEeCCCEEEEEEEEEeC-CCCcccc
Confidence 356789999999988764432 2446666
No 165
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=35.67 E-value=53 Score=16.61 Aligned_cols=16 Identities=25% Similarity=0.131 Sum_probs=12.9
Q ss_pred EEecCCEEEEEEEeCC
Q psy88 6 NVCEGDRVVVDVRNSM 21 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~~ 21 (75)
.++.||.|++.+.+-.
T Consensus 47 ~~~~Gd~v~v~i~~vd 62 (77)
T cd05708 47 LFRVGDKVRAKVLKID 62 (77)
T ss_pred eecCCCEEEEEEEEEe
Confidence 4689999999988754
No 166
>smart00232 JAB_MPN JAB/MPN domain. Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function.
Probab=35.65 E-value=19 Score=20.48 Aligned_cols=7 Identities=29% Similarity=0.928 Sum_probs=5.4
Q ss_pred eEEccCC
Q psy88 69 HFWHAHT 75 (75)
Q Consensus 69 ~~YH~H~ 75 (75)
=|||+|.
T Consensus 80 Gwyhshp 86 (135)
T smart00232 80 GWYHSHP 86 (135)
T ss_pred EEEEcCC
Confidence 4999984
No 167
>PTZ00047 cytochrome c oxidase subunit II; Provisional
Probab=35.45 E-value=1.1e+02 Score=19.06 Aligned_cols=23 Identities=9% Similarity=0.153 Sum_probs=18.3
Q ss_pred cCCCCEEEEEEc-CCCeeeEEccC
Q psy88 52 ITQGNTFRYQFT-ANAGTHFWHAH 74 (75)
Q Consensus 52 i~pG~~~~y~~~-~~~Gt~~YH~H 74 (75)
+-||..-...+. +.+|+|.-.|.
T Consensus 107 avPGr~n~l~~~~~~~G~y~gqCs 130 (162)
T PTZ00047 107 AIPGRLHKINTFILREGVFYGQCS 130 (162)
T ss_pred ccCCceEEEEEecCCCeEEEEEcc
Confidence 457888788787 89999988774
No 168
>cd00184 TNF Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding.
Probab=35.37 E-value=35 Score=19.97 Aligned_cols=16 Identities=31% Similarity=0.418 Sum_probs=13.2
Q ss_pred cEEEecCCEEEEEEEe
Q psy88 4 PKNVCEGDRVVVDVRN 19 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N 19 (75)
.+++++||+|.|.+.+
T Consensus 106 vf~L~~gd~l~v~v~~ 121 (137)
T cd00184 106 LFQLRAGDRLSVNVSA 121 (137)
T ss_pred EEEecCCCEEEEEeCC
Confidence 4688999999998863
No 169
>cd07701 Ig1_Necl-3 First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3, also known as cell adhesion molecule 2 (CADM2)). Ig1_Necl-3: domain similar to the N-terminal immunoglobulin (Ig)-like domain of nectin-like molecule-3, Necl-3 (also known as cell adhesion molecule 2 (CADM2), SynCAM2, IGSF4D). Nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 - Necl-5). They all have an extracellular region containing three Ig-like domains, a transmembrane region, and a cytoplasmic region. The N-terminal Ig-like domain of the extracellular region, belongs to the V-type subfamily of Ig domains, is essential to cell-cell adhesion, and plays a part in the interaction with the envelope glycoprotein D of various viruses. Necl-3 accumulates in central and peripheral nervous system tissue, and has been shown to selectively interact with oligodendrocytes.
Probab=35.06 E-value=79 Score=17.15 Aligned_cols=28 Identities=18% Similarity=0.351 Sum_probs=20.2
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEe
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHW 30 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~ 30 (75)
++.+.+.+|+.+.++=.=... ....+.|
T Consensus 4 ~~~v~v~eG~~v~L~C~~~~~-p~~~v~W 31 (95)
T cd07701 4 TQNVTVVEGGTANLTCRVDQN-DNTSLQW 31 (95)
T ss_pred cceEEEecCCcEEEEEEEecC-CceEEEE
Confidence 356889999999998754433 3456888
No 170
>CHL00084 rpl19 ribosomal protein L19
Probab=35.02 E-value=34 Score=20.21 Aligned_cols=16 Identities=31% Similarity=0.295 Sum_probs=12.7
Q ss_pred EEEecCCEEEEEEEeC
Q psy88 5 KNVCEGDRVVVDVRNS 20 (75)
Q Consensus 5 i~~~~Gd~v~i~~~N~ 20 (75)
-.++.||+|+|.+.-.
T Consensus 21 p~f~~GDtV~V~~~i~ 36 (117)
T CHL00084 21 PKIRVGDTVKVGVLIQ 36 (117)
T ss_pred CccCCCCEEEEEEEEe
Confidence 3678999999999654
No 171
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=34.98 E-value=25 Score=17.80 Aligned_cols=13 Identities=31% Similarity=0.371 Sum_probs=9.6
Q ss_pred cEEEecCCEEEEE
Q psy88 4 PKNVCEGDRVVVD 16 (75)
Q Consensus 4 ~i~~~~Gd~v~i~ 16 (75)
...+++||+|+|-
T Consensus 48 ~~~l~~gD~vei~ 60 (66)
T PRK05659 48 STALREGDVVEIV 60 (66)
T ss_pred cccCCCCCEEEEE
Confidence 3457889998874
No 172
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=34.76 E-value=30 Score=14.10 Aligned_cols=10 Identities=40% Similarity=0.245 Sum_probs=6.9
Q ss_pred EecCCEEEEE
Q psy88 7 VCEGDRVVVD 16 (75)
Q Consensus 7 ~~~Gd~v~i~ 16 (75)
+++||.|+|.
T Consensus 2 ~~~G~~V~I~ 11 (28)
T smart00739 2 FEVGDTVRVI 11 (28)
T ss_pred CCCCCEEEEe
Confidence 3578887775
No 173
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=34.69 E-value=18 Score=21.11 Aligned_cols=8 Identities=25% Similarity=0.812 Sum_probs=6.0
Q ss_pred eeEEccCC
Q psy88 68 THFWHAHT 75 (75)
Q Consensus 68 t~~YH~H~ 75 (75)
.-|||||.
T Consensus 72 vg~yHSHP 79 (134)
T COG1310 72 VGWYHSHP 79 (134)
T ss_pred EEEEcCCC
Confidence 45899984
No 174
>TIGR01451 B_ant_repeat conserved repeat domain. This model represents the conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis, and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydial outer membrane proteins.
Probab=34.62 E-value=35 Score=16.86 Aligned_cols=17 Identities=41% Similarity=0.675 Sum_probs=13.6
Q ss_pred cCCCCEEEEEEc-CCCee
Q psy88 52 ITQGNTFRYQFT-ANAGT 68 (75)
Q Consensus 52 i~pG~~~~y~~~-~~~Gt 68 (75)
+.||+..+|.+. .+.|.
T Consensus 8 ~~~Gd~v~Yti~v~N~g~ 25 (53)
T TIGR01451 8 ATIGDTITYTITVTNNGN 25 (53)
T ss_pred cCCCCEEEEEEEEEECCC
Confidence 689999999998 55553
No 175
>TIGR01024 rplS_bact ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs.
Probab=34.30 E-value=39 Score=19.80 Aligned_cols=17 Identities=29% Similarity=0.280 Sum_probs=13.9
Q ss_pred EEEecCCEEEEEEEeCC
Q psy88 5 KNVCEGDRVVVDVRNSM 21 (75)
Q Consensus 5 i~~~~Gd~v~i~~~N~~ 21 (75)
-.++.||+|.|.+....
T Consensus 17 p~f~~GD~v~V~~~i~e 33 (113)
T TIGR01024 17 PDFRVGDTVRVHVKIVE 33 (113)
T ss_pred CccCCCCEEEEEEEEcc
Confidence 35789999999998754
No 176
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=34.00 E-value=19 Score=17.93 Aligned_cols=14 Identities=21% Similarity=0.453 Sum_probs=8.2
Q ss_pred EEecCCEEEEEEEe
Q psy88 6 NVCEGDRVVVDVRN 19 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N 19 (75)
.+++||+|.+.++-
T Consensus 46 ~L~~G~~V~~~ik~ 59 (64)
T PF03459_consen 46 GLKPGDEVYASIKA 59 (64)
T ss_dssp T-STT-EEEEEE-G
T ss_pred CCCCCCEEEEEEeh
Confidence 45688998887753
No 177
>PF14874 PapD-like: Flagellar-associated PapD-like
Probab=33.50 E-value=84 Score=16.99 Aligned_cols=46 Identities=11% Similarity=0.104 Sum_probs=26.7
Q ss_pred EEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcc--cccccCCCCEEEEEEc
Q psy88 12 RVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFV--TQCPITQGNTFRYQFT 63 (75)
Q Consensus 12 ~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~--~~~~i~pG~~~~y~~~ 63 (75)
...|.++|... .+..+++.-.. . .+..-.+ ....++||++.+....
T Consensus 23 ~~~v~l~N~s~-~p~~f~v~~~~---~--~~~~~~v~~~~g~l~PG~~~~~~V~ 70 (102)
T PF14874_consen 23 SRTVTLTNTSS-IPARFRVRQPE---S--LSSFFSVEPPSGFLAPGESVELEVT 70 (102)
T ss_pred EEEEEEEECCC-CCEEEEEEeCC---c--CCCCEEEECCCCEECCCCEEEEEEE
Confidence 45688889987 67666653211 0 0110000 1224899999998877
No 178
>PF07385 DUF1498: Protein of unknown function (DUF1498); InterPro: IPR010864 This family consists of several hypothetical bacterial proteins of around 225 residues in length. The function of this family is unknown.; PDB: 3MPB_B 3KMH_A.
Probab=33.50 E-value=1.1e+02 Score=20.16 Aligned_cols=50 Identities=22% Similarity=0.258 Sum_probs=23.3
Q ss_pred EEEecCCEEEEEEEeCCCC------CCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEE
Q psy88 5 KNVCEGDRVVVDVRNSMDG------LENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQ 61 (75)
Q Consensus 5 i~~~~Gd~v~i~~~N~~~~------~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~ 61 (75)
|.-+-|-++.|+|.|..+. .+.++..-|..... +.-++..+.||||.|..
T Consensus 112 IINRGGG~L~i~l~~s~~~~~~~~~~~v~V~~DG~~~t~-------~aG~~l~L~PGESiTL~ 167 (225)
T PF07385_consen 112 IINRGGGNLVIELYNSDPDGELDADTDVTVPVDGIRRTV-------PAGTQLRLNPGESITLP 167 (225)
T ss_dssp EEEEEES-EEEEEEEB--TTSSB-SS-EEEEETTEEEEE--------TT-EEEE-TT-EEEE-
T ss_pred eeecCCceEEEEEEeccCCCccccCCCeEEecCCcEEEe-------cCCceEEeCCCCeEeeC
Confidence 4445568899999997531 23344444433221 11124457889988753
No 179
>KOG4680|consensus
Probab=33.49 E-value=43 Score=20.61 Aligned_cols=23 Identities=22% Similarity=0.550 Sum_probs=15.3
Q ss_pred cccccCCCCEE---EEEEc--CCCeeeE
Q psy88 48 TQCPITQGNTF---RYQFT--ANAGTHF 70 (75)
Q Consensus 48 ~~~~i~pG~~~---~y~~~--~~~Gt~~ 70 (75)
+.|||+||+-- +..++ -+||+|.
T Consensus 95 tsCPVepG~f~~~hsq~LPg~tPPG~Y~ 122 (153)
T KOG4680|consen 95 TSCPVEPGDFLVAHSQVLPGYTPPGSYV 122 (153)
T ss_pred ccCCcCcCceeeeeeEeccCcCCCceEE
Confidence 36899998743 44444 5788774
No 180
>cd07767 MPN Mpr1p, Pad1p N-terminal (MPN) domains. MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors. These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. J
Probab=33.30 E-value=21 Score=19.72 Aligned_cols=7 Identities=29% Similarity=0.904 Sum_probs=5.1
Q ss_pred eEEccCC
Q psy88 69 HFWHAHT 75 (75)
Q Consensus 69 ~~YH~H~ 75 (75)
=|||+|.
T Consensus 67 Gwyhshp 73 (116)
T cd07767 67 GWYHTHP 73 (116)
T ss_pred EEEEcCC
Confidence 4888883
No 181
>COG4013 Uncharacterized protein conserved in archaea [Function unknown]
Probab=33.22 E-value=32 Score=19.30 Aligned_cols=13 Identities=31% Similarity=0.215 Sum_probs=10.5
Q ss_pred EEecCCEEEEEEE
Q psy88 6 NVCEGDRVVVDVR 18 (75)
Q Consensus 6 ~~~~Gd~v~i~~~ 18 (75)
++++||+|++.+-
T Consensus 20 eV~~gd~vel~~g 32 (91)
T COG4013 20 EVDVGDYVELYFG 32 (91)
T ss_pred cCCCCCEEEEEEE
Confidence 4789999999764
No 182
>COG1917 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=32.96 E-value=59 Score=18.60 Aligned_cols=24 Identities=17% Similarity=0.181 Sum_probs=16.8
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEeCCc
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHWHGI 33 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~ 33 (75)
.+..++++||.+.+ .+-..||++.
T Consensus 81 g~~~~l~~Gd~i~i--------p~g~~H~~~a 104 (131)
T COG1917 81 GEKKELKAGDVIII--------PPGVVHGLKA 104 (131)
T ss_pred CCceEecCCCEEEE--------CCCCeeeecc
Confidence 35677888888887 3557777664
No 183
>PF00018 SH3_1: SH3 domain; InterPro: IPR001452 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. The crystal structure of the SH3 domain of the cytoskeletal protein spectrin, and the solution structures of SH3 domains of phospholipase C (PLC-y) and phosphatidylinositol 3-kinase p85 alpha-subunit, have been determined [, , ]. In spite of relatively limited sequence similarity, their overall structures are similar. The domains belong to the alpha+beta structural class, with 5 to 8 beta-strands forming 2 tightly-packed, anti-parallel beta-sheets arranged in a barrel-like structure, and intervening loops sometimes forming helices. Conserved aliphatic and aromatic residues form a hydrophobic core (A11, L23, A29, V34, W42, L52 and V59 in PLC-y []) and a hydrophobic pocket on the molecular surface (L12, F13, W53 and P55 in PLC-y). The conserved core is believed to stabilise the fold, while the pocket is thought to serve as a binding site for target proteins. Conserved carboxylic amino acids located in the loops, on the periphery of the pocket (D14 and E22), may be involved in protein-protein interactions via proline-rich regions. The N- and C-termini are packed in close proximity, indicating that they are independent structural modules.; GO: 0005515 protein binding; PDB: 1UHF_A 1W1F_A 1WA7_A 1SEM_A 1KFZ_A 2SEM_B 1K76_A 3SEM_B 1X2Q_A 2J06_B ....
Probab=32.91 E-value=19 Score=17.09 Aligned_cols=14 Identities=21% Similarity=0.086 Sum_probs=10.0
Q ss_pred ccEEEecCCEEEEE
Q psy88 3 YPKNVCEGDRVVVD 16 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~ 16 (75)
..|.+++||.+.|.
T Consensus 12 ~eLs~~~Gd~i~v~ 25 (48)
T PF00018_consen 12 DELSFKKGDIIEVL 25 (48)
T ss_dssp TBSEB-TTEEEEEE
T ss_pred CEEeEECCCEEEEE
Confidence 35778999998874
No 184
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=32.83 E-value=43 Score=17.80 Aligned_cols=14 Identities=14% Similarity=0.404 Sum_probs=11.3
Q ss_pred EEecCCEEEEEEEe
Q psy88 6 NVCEGDRVVVDVRN 19 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N 19 (75)
++..||.+.+.++|
T Consensus 56 ~a~aGd~v~~~l~~ 69 (83)
T cd03698 56 YAVAGENVRLKLKG 69 (83)
T ss_pred EECCCCEEEEEECC
Confidence 47789999988876
No 185
>cd08066 MPN_AMSH_like Mov34/MPN/PAD-1 family. AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM (signal-transducing adapter molecule, also known as STAMBP)) and AMSH-like proteins (AMSH-LP) are members of JAMM/MPN+ deubiquitinases (DUBs), with Zn2+-dependent ubiquitin isopeptidase activity. AMSH specifically cleaves Lys 63 and not Lys48-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. AMSH and AMSH-LP are anchored on the early endosomal membrane via interaction with the clathrin coat. AMSH shares a common SH3-binding site with another endosomal DUB, UBPY (ubiquitin-specific protease Y; also known as USP8), the latter being a cysteine protease that does not discriminate between Lys48 and Lys63-linked ubiquitin. AMSH is involved in the degradation of EGF receptor (EGFR) and possibly other ubiquitinated endocytosed proteins. AMSH also interacts with CHMP1, CHMP2, and CHMP3 proteins, al
Probab=32.79 E-value=21 Score=22.19 Aligned_cols=7 Identities=29% Similarity=0.624 Sum_probs=5.6
Q ss_pred eEEccCC
Q psy88 69 HFWHAHT 75 (75)
Q Consensus 69 ~~YH~H~ 75 (75)
=|||+|.
T Consensus 79 GwyHSHP 85 (173)
T cd08066 79 GWIHTHP 85 (173)
T ss_pred EEEeccC
Confidence 4999994
No 186
>PRK11347 antitoxin ChpS; Provisional
Probab=32.68 E-value=33 Score=18.82 Aligned_cols=16 Identities=31% Similarity=0.383 Sum_probs=13.1
Q ss_pred EEEecCCEEEEEEEeC
Q psy88 5 KNVCEGDRVVVDVRNS 20 (75)
Q Consensus 5 i~~~~Gd~v~i~~~N~ 20 (75)
+.++.||+|.|.+.+.
T Consensus 24 l~l~~G~~v~i~v~~~ 39 (83)
T PRK11347 24 LNLQPGQSVEAQVSNN 39 (83)
T ss_pred cCCCCCCEEEEEEECC
Confidence 5577899999998875
No 187
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=32.65 E-value=30 Score=18.72 Aligned_cols=13 Identities=38% Similarity=0.297 Sum_probs=10.1
Q ss_pred EEEecCCEEEEEE
Q psy88 5 KNVCEGDRVVVDV 17 (75)
Q Consensus 5 i~~~~Gd~v~i~~ 17 (75)
+.++.||+|.|--
T Consensus 5 ~~I~kGD~V~Vi~ 17 (76)
T PRK12281 5 LKVKKGDMVKVIA 17 (76)
T ss_pred ccccCCCEEEEeE
Confidence 5788999988754
No 188
>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=32.62 E-value=50 Score=18.02 Aligned_cols=16 Identities=31% Similarity=0.681 Sum_probs=13.6
Q ss_pred cccccCCCCEEEEEEc
Q psy88 48 TQCPITQGNTFRYQFT 63 (75)
Q Consensus 48 ~~~~i~pG~~~~y~~~ 63 (75)
...++.+|..|.|++.
T Consensus 32 ~T~~L~~G~~y~Y~v~ 47 (75)
T TIGR03000 32 TTPPLEAGKEYEYTVT 47 (75)
T ss_pred ECCCCCCCCEEEEEEE
Confidence 3567999999999998
No 189
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=32.61 E-value=25 Score=19.47 Aligned_cols=11 Identities=27% Similarity=0.613 Sum_probs=9.3
Q ss_pred EEecCCEEEEE
Q psy88 6 NVCEGDRVVVD 16 (75)
Q Consensus 6 ~~~~Gd~v~i~ 16 (75)
.+++||.|+|.
T Consensus 50 ~~~~GD~V~I~ 60 (84)
T CHL00142 50 ECNIGDQVLIE 60 (84)
T ss_pred CCCCCCEEEEE
Confidence 47899999986
No 190
>smart00318 SNc Staphylococcal nuclease homologues.
Probab=32.28 E-value=80 Score=18.09 Aligned_cols=33 Identities=27% Similarity=0.317 Sum_probs=24.6
Q ss_pred ccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCC
Q psy88 3 YPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGT 38 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~ 38 (75)
...++--||+++|.+.+. ....+-+-|+..+..
T Consensus 6 ~V~~V~DGDT~~v~~~~~---~~~~vrL~gIdaPe~ 38 (138)
T smart00318 6 VVERVLDGDTIRVRLPKN---KLITIRLSGIDAPET 38 (138)
T ss_pred EEEEEecCCEEEEEeCCC---CEEEEEEEeccCCcc
Confidence 356788999999987543 357888899987643
No 191
>cd05794 S1_EF-P_repeat_2 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P
Probab=32.12 E-value=41 Score=17.20 Aligned_cols=13 Identities=38% Similarity=0.713 Sum_probs=9.9
Q ss_pred cEEEecCCEEEEE
Q psy88 4 PKNVCEGDRVVVD 16 (75)
Q Consensus 4 ~i~~~~Gd~v~i~ 16 (75)
|+-+++||.|+|.
T Consensus 35 P~FI~~Gd~I~V~ 47 (56)
T cd05794 35 PLFIKEGEKIKVD 47 (56)
T ss_pred CCeecCCCEEEEE
Confidence 4557899998885
No 192
>PF01398 JAB: JAB1/Mov34/MPN/PAD-1 ubiquitin protease; InterPro: IPR000555 Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This family is also known as the MPN domain [] and PAD-1-like domain []. It has been shown that this domain occurs in prokaryotes []. Mov34 proteins act as the regulatory subunit of the 26 proteasome, which is involved in the ATP-dependent degradation of ubiquitinated proteins. The function of this domain is unclear, but it is found in the N terminus of the proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. A number of the proteins associated with this family belong to MEROPS peptidase family M67 (clan M-). This includes the Poh1 peptidase of Saccharomyces cerevisiae (Baker's yeast) which is a component of the 19S proteasome regulatory particle.; GO: 0005515 protein binding; PDB: 2ZNV_D 2ZNR_A 4E0Q_A 2P87_A 2P8R_A 2O96_B 2O95_A 3RZU_F 3RZV_A.
Probab=31.88 E-value=19 Score=20.22 Aligned_cols=6 Identities=33% Similarity=1.077 Sum_probs=4.3
Q ss_pred eEEccC
Q psy88 69 HFWHAH 74 (75)
Q Consensus 69 ~~YH~H 74 (75)
=|||+|
T Consensus 85 GWY~s~ 90 (114)
T PF01398_consen 85 GWYHSH 90 (114)
T ss_dssp EEEEEE
T ss_pred EEEEcc
Confidence 478876
No 193
>cd08069 MPN_RPN11_CSN5 Mov34/MPN/PAD-1 family: proteasomal regulatory protein Rpn11 and signalosome complex subunit CSN5. This family contains proteasomal regulatory protein Rpn11 (26S proteasome regulatory subunit rpn11; PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the 19S-proteasome; regulatory particle number 11) and signalosomal CSN5 (COP9 signalosome complex subunit 5; COP9 complex homolog subunit 5; c-Jun activation domain-binding protein-1; CSN5/JAB1; JAB1). COP9 signalosome (CSN) and the proteasome lid are paralogous complexes and their respective subunits CSN5 and Rpn11 are most closely related between the two complexes, both containing the conserved JAMM (JAB1/MPN/Mov34 metalloenzyme) motif involved in zinc ion coordination and providing the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology; mutations i
Probab=31.84 E-value=22 Score=23.65 Aligned_cols=8 Identities=25% Similarity=0.812 Sum_probs=5.9
Q ss_pred eeEEccCC
Q psy88 68 THFWHAHT 75 (75)
Q Consensus 68 t~~YH~H~ 75 (75)
.=|||+|.
T Consensus 90 VGWYHSHP 97 (268)
T cd08069 90 VGWYHSHP 97 (268)
T ss_pred EeeeccCC
Confidence 34999984
No 194
>PHA03189 UL14 tegument protein; Provisional
Probab=31.79 E-value=90 Score=21.76 Aligned_cols=18 Identities=17% Similarity=0.351 Sum_probs=12.4
Q ss_pred cCCCCEEEEEEc---CCCeee
Q psy88 52 ITQGNTFRYQFT---ANAGTH 69 (75)
Q Consensus 52 i~pG~~~~y~~~---~~~Gt~ 69 (75)
+.+.+.++.+|. +.+|+|
T Consensus 128 lg~aq~ltLtF~v~t~taG~Y 148 (348)
T PHA03189 128 LGAAQRLTLTFRVSTSTAGMY 148 (348)
T ss_pred ccceeEEEEEEEEEecccceE
Confidence 445677788887 667765
No 195
>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=31.70 E-value=50 Score=15.65 Aligned_cols=42 Identities=14% Similarity=0.180 Sum_probs=22.2
Q ss_pred EEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEE
Q psy88 15 VDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQF 62 (75)
Q Consensus 15 i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~ 62 (75)
+.|+|..+ .+..|- .+...... . .+.....+|+||++....+
T Consensus 2 F~~~N~g~-~~L~I~--~v~tsCgC-t--~~~~~~~~i~PGes~~i~v 43 (45)
T PF07610_consen 2 FEFTNTGD-SPLVIT--DVQTSCGC-T--TAEYSKKPIAPGESGKIKV 43 (45)
T ss_pred EEEEECCC-CcEEEE--EeeEccCC-E--EeeCCcceECCCCEEEEEE
Confidence 57788877 555442 22221110 0 1122345699999987654
No 196
>PF14604 SH3_9: Variant SH3 domain; PDB: 2CRE_A 2E5K_A 2CT3_A 2DE0_X 2D8H_A 2DA9_A 2X3X_E 2X3W_D 2KRN_A 2ED0_A ....
Probab=31.62 E-value=30 Score=16.69 Aligned_cols=14 Identities=21% Similarity=0.140 Sum_probs=10.0
Q ss_pred ccEEEecCCEEEEE
Q psy88 3 YPKNVCEGDRVVVD 16 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~ 16 (75)
..|.+++||.|.|.
T Consensus 11 dELs~~~Gd~i~v~ 24 (49)
T PF14604_consen 11 DELSFKKGDVITVL 24 (49)
T ss_dssp TB-EB-TTEEEEEE
T ss_pred CEeeEcCCCEEEEE
Confidence 45888999999987
No 197
>PLN00208 translation initiation factor (eIF); Provisional
Probab=31.55 E-value=46 Score=20.40 Aligned_cols=17 Identities=24% Similarity=0.429 Sum_probs=13.8
Q ss_pred cEEEecCCEEEEEEEeC
Q psy88 4 PKNVCEGDRVVVDVRNS 20 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~ 20 (75)
-|++++||.|.|.+.-.
T Consensus 68 rIWI~~GD~VlVel~~~ 84 (145)
T PLN00208 68 KVWIAAGDIILVGLRDY 84 (145)
T ss_pred eEEecCCCEEEEEccCC
Confidence 48899999999986544
No 198
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=31.28 E-value=39 Score=18.44 Aligned_cols=20 Identities=25% Similarity=0.228 Sum_probs=15.4
Q ss_pred cccEEEecCCEEEEEEEeCC
Q psy88 2 LYPKNVCEGDRVVVDVRNSM 21 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~ 21 (75)
+.-|.+|.||.|.|.=.+..
T Consensus 1 P~FL~Vk~Gd~ViV~~~~~~ 20 (75)
T PF11302_consen 1 PVFLSVKPGDTVIVQDEQEV 20 (75)
T ss_pred CcccccCCCCEEEEecCccc
Confidence 35678999999999876643
No 199
>PF11614 FixG_C: IG-like fold at C-terminal of FixG, putative oxidoreductase; PDB: 2R39_A.
Probab=31.14 E-value=88 Score=17.63 Aligned_cols=45 Identities=16% Similarity=0.220 Sum_probs=19.8
Q ss_pred EEEEEEeCCCCCCce--EEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc
Q psy88 13 VVVDVRNSMDGLENT--IHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT 63 (75)
Q Consensus 13 v~i~~~N~~~~~~~~--iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~ 63 (75)
-++.+.|+.. .+.. |=.-|+. ......+.. ...|+||++....+.
T Consensus 35 Y~lkl~Nkt~-~~~~~~i~~~g~~--~~~l~~~~~---~i~v~~g~~~~~~v~ 81 (118)
T PF11614_consen 35 YTLKLTNKTN-QPRTYTISVEGLP--GAELQGPEN---TITVPPGETREVPVF 81 (118)
T ss_dssp EEEEEEE-SS-S-EEEEEEEES-S--S-EE-ES-----EEEE-TT-EEEEEEE
T ss_pred EEEEEEECCC-CCEEEEEEEecCC--CeEEECCCc---ceEECCCCEEEEEEE
Confidence 4688889876 4433 3333321 110001112 234789999888876
No 200
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=31.12 E-value=71 Score=16.10 Aligned_cols=16 Identities=38% Similarity=0.225 Sum_probs=12.7
Q ss_pred EEecCCEEEEEEEeCC
Q psy88 6 NVCEGDRVVVDVRNSM 21 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~~ 21 (75)
..+.||.+++.+....
T Consensus 48 ~~~~Gd~v~v~v~~id 63 (72)
T cd05689 48 VVSLGDEVEVMVLDID 63 (72)
T ss_pred EeCCCCEEEEEEEEee
Confidence 3688999999987754
No 201
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=30.87 E-value=45 Score=20.70 Aligned_cols=16 Identities=25% Similarity=0.393 Sum_probs=13.3
Q ss_pred cEEEecCCEEEEEEEe
Q psy88 4 PKNVCEGDRVVVDVRN 19 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N 19 (75)
-|++++||.|.|.+.=
T Consensus 68 ~IWI~~GD~VlVel~~ 83 (155)
T PTZ00329 68 RVWINIGDIILVSLRD 83 (155)
T ss_pred eEEecCCCEEEEeccC
Confidence 4899999999998643
No 202
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=30.63 E-value=75 Score=15.74 Aligned_cols=15 Identities=27% Similarity=0.098 Sum_probs=12.1
Q ss_pred EEecCCEEEEEEEeC
Q psy88 6 NVCEGDRVVVDVRNS 20 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~ 20 (75)
.++.||.|++.+..-
T Consensus 45 ~~~~G~~v~v~v~~i 59 (69)
T cd05690 45 IYKKGQEVEAVVLNI 59 (69)
T ss_pred EECCCCEEEEEEEEE
Confidence 368899999998764
No 203
>smart00205 THN Thaumatin family. The thaumatin family gathers proteins related to plant pathogenesis. The thaumatin family includes very basic members with extracellular and vacuolar localization. Thaumatin itsel is a potent sweet-tasting protein. Several members of this family display significant in vitro activity of inhibiting hyphal growth or spore germination of various fungi probably by a membrane permeabilizing mechanism.
Probab=30.40 E-value=1.6e+02 Score=19.23 Aligned_cols=20 Identities=10% Similarity=0.380 Sum_probs=15.6
Q ss_pred ccCCCCEEEEEEc-CC-CeeeE
Q psy88 51 PITQGNTFRYQFT-AN-AGTHF 70 (75)
Q Consensus 51 ~i~pG~~~~y~~~-~~-~Gt~~ 70 (75)
.+.||+++++..+ .- +|.+|
T Consensus 29 ~L~~g~s~~~~~p~~w~sGriW 50 (218)
T smart00205 29 ELNSGASWQLDAPPGTKMGRIW 50 (218)
T ss_pred ecCCCCeEEEECCCCCccceEe
Confidence 4889999999988 44 37666
No 204
>cd05891 Ig_M-protein_C C-terminal immunoglobulin (Ig)-like domain of M-protein (also known as myomesin-2). Ig_M-protein_C: the C-terminal immunoglobulin (Ig)-like domain of M-protein (also known as myomesin-2). M-protein is a structural protein localized to the M-band, a transverse structure in the center of the sarcomere, and is a candidate for M-band bridges. M-protein is modular consisting mainly of repetitive IG-like and fibronectin type III (FnIII) domains, and has a muscle-type specific expression pattern. M-protein is present in fast fibers.
Probab=30.30 E-value=94 Score=16.58 Aligned_cols=28 Identities=11% Similarity=0.169 Sum_probs=19.0
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEe
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHW 30 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~ 30 (75)
+..+.+.+|+.+++.-.=... ....+.|
T Consensus 8 p~~v~v~eG~~v~L~C~v~g~-P~p~i~W 35 (92)
T cd05891 8 PDVVTIMEGKTLNLTCTVFGN-PDPEVIW 35 (92)
T ss_pred CCcEEEcCCCEEEEEEEEEEe-CCCeEEE
Confidence 457889999999988752222 2335777
No 205
>smart00326 SH3 Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
Probab=30.14 E-value=34 Score=15.86 Aligned_cols=17 Identities=18% Similarity=0.141 Sum_probs=12.3
Q ss_pred ccEEEecCCEEEEEEEe
Q psy88 3 YPKNVCEGDRVVVDVRN 19 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N 19 (75)
..|.+++||.|.+.-..
T Consensus 17 ~~l~~~~Gd~v~v~~~~ 33 (58)
T smart00326 17 DELSFKKGDIITVLEKS 33 (58)
T ss_pred CCCCCCCCCEEEEEEcC
Confidence 34677899998887543
No 206
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=30.04 E-value=54 Score=17.24 Aligned_cols=17 Identities=24% Similarity=0.366 Sum_probs=12.6
Q ss_pred EEEecCCEEEEEEEeCC
Q psy88 5 KNVCEGDRVVVDVRNSM 21 (75)
Q Consensus 5 i~~~~Gd~v~i~~~N~~ 21 (75)
+++..||.|.+.+....
T Consensus 45 i~i~vGD~V~ve~~~~~ 61 (72)
T PRK00276 45 IRILPGDKVTVELSPYD 61 (72)
T ss_pred cccCCCCEEEEEEcccC
Confidence 45678999999876543
No 207
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=30.01 E-value=76 Score=15.43 Aligned_cols=15 Identities=40% Similarity=0.330 Sum_probs=12.1
Q ss_pred EEecCCEEEEEEEeC
Q psy88 6 NVCEGDRVVVDVRNS 20 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~ 20 (75)
.++.||.+++.+..-
T Consensus 44 ~~~~Gd~v~v~i~~v 58 (68)
T cd05688 44 VVNVGDEVEVKVLKI 58 (68)
T ss_pred EECCCCEEEEEEEEE
Confidence 368999999988764
No 208
>PF03423 CBM_25: Carbohydrate binding domain (family 25); InterPro: IPR005085 A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins. CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [, ]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology. Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see []. This entry represents CBM25 from CAZY which has a starch-binding function as has been demonstrated in one case.; PDB: 2LAB_A 2C3X_B 2C3V_A 2C3W_C 2LAA_A.
Probab=29.97 E-value=76 Score=17.29 Aligned_cols=24 Identities=25% Similarity=0.401 Sum_probs=13.6
Q ss_pred CCEEEEEEE---eCCCCCCceEEeCCcc
Q psy88 10 GDRVVVDVR---NSMDGLENTIHWHGIH 34 (75)
Q Consensus 10 Gd~v~i~~~---N~~~~~~~~iH~HG~~ 34 (75)
|++|+|.+. ..+. ....||.|+-.
T Consensus 1 G~~vtVyYn~~~~~l~-g~~~v~~~~G~ 27 (87)
T PF03423_consen 1 GETVTVYYNPSLTALS-GAPNVHLHGGF 27 (87)
T ss_dssp -SEEEEEE---E-SSS--S-EEEEEETT
T ss_pred CCEEEEEEEeCCCCCC-CCCcEEEEecC
Confidence 788888883 2233 36688988854
No 209
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=29.83 E-value=74 Score=16.07 Aligned_cols=14 Identities=36% Similarity=0.617 Sum_probs=10.0
Q ss_pred EEecCCEEEEEEEe
Q psy88 6 NVCEGDRVVVDVRN 19 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N 19 (75)
++..||.|.+.+..
T Consensus 40 ~~~vGD~V~~~~~~ 53 (64)
T cd04451 40 RILPGDRVKVELSP 53 (64)
T ss_pred ccCCCCEEEEEEee
Confidence 45678888887664
No 210
>PF06030 DUF916: Bacterial protein of unknown function (DUF916); InterPro: IPR010317 This family consists of putative cell surface proteins, from Firmicutes, of unknown function.
Probab=29.79 E-value=1.2e+02 Score=17.65 Aligned_cols=14 Identities=14% Similarity=0.252 Sum_probs=11.8
Q ss_pred cccCCCCEEEEEEc
Q psy88 50 CPITQGNTFRYQFT 63 (75)
Q Consensus 50 ~~i~pG~~~~y~~~ 63 (75)
.-|+|+++++..|.
T Consensus 87 Vtl~~~~sk~V~~~ 100 (121)
T PF06030_consen 87 VTLPPNESKTVTFT 100 (121)
T ss_pred EEECCCCEEEEEEE
Confidence 44889999999887
No 211
>KOG4792|consensus
Probab=29.70 E-value=34 Score=22.90 Aligned_cols=19 Identities=26% Similarity=0.172 Sum_probs=15.9
Q ss_pred cEEEecCCEEEEEEEeCCC
Q psy88 4 PKNVCEGDRVVVDVRNSMD 22 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~ 22 (75)
-|+++.||.|.|+=+|.-.
T Consensus 245 aL~levGdiVkVTk~ninG 263 (293)
T KOG4792|consen 245 ALALEVGDIVKVTKKNING 263 (293)
T ss_pred hhhhhcCcEEEEEeeccCc
Confidence 4789999999999888643
No 212
>KOG4458|consensus
Probab=29.62 E-value=39 Score=18.07 Aligned_cols=28 Identities=14% Similarity=0.237 Sum_probs=21.6
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEe
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHW 30 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~ 30 (75)
++-|.+..|--.+|-+.|.+. ..+-||+
T Consensus 9 pydii~dd~~d~riplhne~a-~qhgi~f 36 (78)
T KOG4458|consen 9 PYDIIADDGHDCRIPLHNEDA-FQHGICF 36 (78)
T ss_pred Ccceeecccccceeeccchhh-hhccceE
Confidence 466788889999999999987 5655544
No 213
>PF05896 NQRA: Na(+)-translocating NADH-quinone reductase subunit A (NQRA); InterPro: IPR008703 This family consists of several bacterial Na+-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na+-translocating NADH: ubiquinone oxidoreductase (Na+-NQR) generates an electrochemical Na+ potential driven by aerobic respiration [].; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0006814 sodium ion transport, 0055114 oxidation-reduction process
Probab=29.54 E-value=44 Score=22.38 Aligned_cols=14 Identities=50% Similarity=0.382 Sum_probs=10.7
Q ss_pred CcccEEEecCCEEE
Q psy88 1 MLYPKNVCEGDRVV 14 (75)
Q Consensus 1 ~~~~i~~~~Gd~v~ 14 (75)
|-+++.+++||+|+
T Consensus 39 ~~Pkm~VkeGD~Vk 52 (257)
T PF05896_consen 39 MKPKMLVKEGDRVK 52 (257)
T ss_pred CCccEEeccCCEEe
Confidence 34678888898886
No 214
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=29.45 E-value=31 Score=19.08 Aligned_cols=11 Identities=27% Similarity=0.193 Sum_probs=9.2
Q ss_pred EEecCCEEEEE
Q psy88 6 NVCEGDRVVVD 16 (75)
Q Consensus 6 ~~~~Gd~v~i~ 16 (75)
.++.||.|+|.
T Consensus 53 ~~k~GD~V~I~ 63 (84)
T PRK05610 53 EAKIGDVVRIM 63 (84)
T ss_pred CCCCCCEEEEE
Confidence 47899999986
No 215
>PF01828 Peptidase_A4: Peptidase A4 family; InterPro: IPR000250 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. The peptidases in family G1 form a subset of what were formerly termed 'pepstatin-insensitive carboxyl proteinases'. After its discovery in about 1970, the pentapeptide pepstatin soon came to be thought of as a very general inhibitor of the endopeptidases that are active at acidic pH. But more recently several acid-acting endopeptidases from bacteria and fungi had been found to be resistant to pepstatin. The unusual active sites of the 'pepstatin-insensitive carboxyl peptidases' proved difficult to characterise, but it has now been established that the enzymes from bacteria are acid-acting serine peptidases in family S53 (clan SB), IPR000209 from INTERPRO, whereas the fungal enzymes are in family G1 (formerly A4). The importance of glutamate ('E') and glutamine ('Q') residues in the active sites of the family G1 enzymes led to the family name, Eqolisin []. This group of glutamate/glutamine peptidases belong to MEROPS peptidase family G1 (eqolisin family, clan GA). An example of this group is scytalidoglutamic peptidase. The proteins are thermostable, pepstatin insensitive and are active at low pH ranges []. The enzyme has a unique heterodimeric structure, with a 39-residue light chain and a 173-residue heavy chain bound to each other non-covalently []. The tertiary structure of the active site of scytalidoglutamic peptidase (MEROPS G01.001) with a bound tripeptide product has been interpreted as showing that Glu136 is the primary catalytic residue. The most likely mechanism is suggested to be nucleophilic attack by a water molecule activated by the Glu136 side chain on the si-face of the scissile peptide bond carbon atom to form the tetrahedral intermediate. Electrophilic assistance, and oxyanion stabilisation, are provided by the side-chain amide of Gln53. Both scytalidoglutamic peptidase (MEROPS G01.001) and aspergilloglutamic peptidase (MEROPS G01.002) cleave the Tyr26 Thr27 bond in the B chain of oxidized insulin; a bond not cleaved by other acid-acting endopeptidases. Scytalidoglutamic peptidase is most active on casein at pH 2 and is inhibited by 1,2-epoxy-3-(p-nitrophenoxy)propane (EPNP), a compound that also inhibits pepsin. ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis; PDB: 1Y43_B 1S2B_A 2IFR_A 1S2K_A 2IFW_A.
Probab=29.44 E-value=46 Score=21.38 Aligned_cols=18 Identities=28% Similarity=0.364 Sum_probs=10.6
Q ss_pred EEEecCCEEEEEEEeCCC
Q psy88 5 KNVCEGDRVVVDVRNSMD 22 (75)
Q Consensus 5 i~~~~Gd~v~i~~~N~~~ 22 (75)
+.++.||.|++++.....
T Consensus 89 ~~v~~GD~i~~~V~a~s~ 106 (208)
T PF01828_consen 89 FPVSPGDTIRVTVTATSN 106 (208)
T ss_dssp ----TT-EEEEEEEEEET
T ss_pred ceECCCCEEEEEEEecCC
Confidence 678999999999986543
No 216
>MTH00023 COX2 cytochrome c oxidase subunit II; Validated
Probab=29.27 E-value=1.7e+02 Score=19.16 Aligned_cols=56 Identities=14% Similarity=0.132 Sum_probs=33.1
Q ss_pred cEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEccC
Q psy88 4 PKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHAH 74 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~H 74 (75)
.|.+-.|..|++.++-.. .| |+...+.. |+ .. -.-||..-...+. +++|.|.-.|.
T Consensus 152 ~lvlP~~~~v~~~~tS~D-----Vi--Hsf~iP~l----gv---K~-DaiPG~~n~~~~~~~~~G~y~g~C~ 208 (240)
T MTH00023 152 RLVVPINTHVRILVTGAD-----VL--HSFAVPSL----GL---KI-DAVPGRLNQTGFFIKRPGVFYGQCS 208 (240)
T ss_pred eEEEecCCEEEEEEEcCC-----cc--cceeeccc----Cc---ee-ecCCCcceeEEEEcCCCEEEEEEch
Confidence 466667777777776552 22 33333311 11 11 1447888777888 88998887773
No 217
>cd04089 eRF3_II eRF3_II: domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-li
Probab=29.18 E-value=53 Score=17.40 Aligned_cols=14 Identities=14% Similarity=0.321 Sum_probs=10.8
Q ss_pred EEecCCEEEEEEEe
Q psy88 6 NVCEGDRVVVDVRN 19 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N 19 (75)
++..||.+.|.++|
T Consensus 55 ~a~aGd~v~l~l~~ 68 (82)
T cd04089 55 YARPGENVRLRLKG 68 (82)
T ss_pred EECCCCEEEEEecC
Confidence 46778888888875
No 218
>PF08940 DUF1918: Domain of unknown function (DUF1918); InterPro: IPR015035 This domain is found in various hypothetical bacterial proteins, and has no known function. ; PDB: 2A7Y_A.
Probab=29.17 E-value=29 Score=17.99 Aligned_cols=12 Identities=42% Similarity=0.642 Sum_probs=6.6
Q ss_pred EEEecCCEEEEE
Q psy88 5 KNVCEGDRVVVD 16 (75)
Q Consensus 5 i~~~~Gd~v~i~ 16 (75)
++++.||++.+.
T Consensus 1 M~A~vGD~lvv~ 12 (58)
T PF08940_consen 1 MHASVGDRLVVH 12 (58)
T ss_dssp ----TTEEEEES
T ss_pred CCCCCCCEEEEc
Confidence 367889998875
No 219
>PF13218 DUF4026: Protein of unknown function (DUF4026)
Probab=29.10 E-value=62 Score=22.45 Aligned_cols=25 Identities=12% Similarity=0.260 Sum_probs=17.6
Q ss_pred cccCCCCEEEEEEc---C-----CCeeeEEccC
Q psy88 50 CPITQGNTFRYQFT---A-----NAGTHFWHAH 74 (75)
Q Consensus 50 ~~i~pG~~~~y~~~---~-----~~Gt~~YH~H 74 (75)
..+.|.=..-|.+. + .++.+|+|.|
T Consensus 147 s~v~Ps~d~LYtihaVyd~D~~~~~~~~WfHTH 179 (323)
T PF13218_consen 147 SDVLPSIDSLYTIHAVYDEDEDPEPTEYWFHTH 179 (323)
T ss_pred cCCCCCccceEEEEEecccccCCCCceEEEEcc
Confidence 45777555556554 3 4799999998
No 220
>cd04975 Ig4_SCFR_like Fourth immunoglobulin (Ig)-like domain of stem cell factor receptor (SCFR) and similar proteins. Ig4_SCFR_like; fourth immunoglobulin (Ig)-like domain of stem cell factor receptor (SCFR). In addition to SCFR this group also includes the fourth Ig domain of platelet-derived growth factor receptors (PDGFR), alpha and beta, the fourth Ig domain of macrophage colony stimulating factor (M-CSF), and the Ig domain of the receptor tyrosine kinase KIT. SCFR and the PDGFR alpha and beta have similar organization: an extracellular component having five Ig-like domains, a transmembrane segment, and a cytoplasmic portion having protein tyrosine kinase activity. SCFR and its ligand SCF are critical for normal hematopoiesis, mast cell development, melanocytes and gametogenesis. SCF binds to the second and third Ig-like domains of SCFR, this fourth Ig-like domain participates in SCFR dimerization, which follows ligand binding. Deletion of this fourth SCFR_Ig-like domain abolishes
Probab=29.07 E-value=1.1e+02 Score=16.94 Aligned_cols=27 Identities=19% Similarity=0.196 Sum_probs=19.5
Q ss_pred ccEEEecCCEEEEEEEeCC-CCCCceEEe
Q psy88 3 YPKNVCEGDRVVVDVRNSM-DGLENTIHW 30 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N~~-~~~~~~iH~ 30 (75)
..+.+++|+.+++...=.. + .+-.+-|
T Consensus 11 ~~~~v~~G~~v~L~c~v~g~~-P~p~v~W 38 (101)
T cd04975 11 TTIFVNLGENLNLVVEVEAYP-PPPHINW 38 (101)
T ss_pred ceEEEECCCCEEEEEEEEecC-CCCccEE
Confidence 4678999999999988766 4 3334555
No 221
>PF09478 CBM49: Carbohydrate binding domain CBM49; InterPro: IPR019028 A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins. CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [, ]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology. Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see []. This domain is found at the C-terminal of cellulases and in vitro binding studies have shown it to binds to crystalline cellulose []. ; GO: 0030246 carbohydrate binding, 0005576 extracellular region
Probab=29.04 E-value=57 Score=17.38 Aligned_cols=13 Identities=23% Similarity=0.723 Sum_probs=10.9
Q ss_pred ccCCCCEEEEEEc
Q psy88 51 PITQGNTFRYQFT 63 (75)
Q Consensus 51 ~i~pG~~~~y~~~ 63 (75)
+|+||+++++-+.
T Consensus 66 ~i~pg~s~~FGYI 78 (80)
T PF09478_consen 66 TIKPGQSFTFGYI 78 (80)
T ss_pred ccCCCCEEEEEEE
Confidence 6899999998764
No 222
>cd05762 Ig8_MLCK Eighth immunoglobulin (Ig)-like domain of human myosin light-chain kinase (MLCK). Ig8_MLCK: the eighth immunoglobulin (Ig)-like domain of human myosin light-chain kinase (MLCK). MLCK is a key regulator of different forms of cell motility involving actin and myosin II. Agonist stimulation of smooth muscle cells increases cytosolic Ca2+, which binds calmodulin. This Ca2+-calmodulin complex in turn binds to and activates MLCK. Activated MLCK leads to the phosphorylation of the 20 kDa myosin regulatory light chain (RLC) of myosin II and the stimulation of actin-activated myosin MgATPase activity. MLCK is widely present in vertebrate tissues; it phosphorylates the 20 kDa RLC of both smooth and nonmuscle myosin II. Phosphorylation leads to the activation of the myosin motor domain and altered structural properties of myosin II. In smooth muscle MLCK it is involved in initiating contraction. In nonmuscle cells, MLCK may participate in cell division and cell motility; it has
Probab=29.02 E-value=1.1e+02 Score=16.71 Aligned_cols=28 Identities=18% Similarity=0.141 Sum_probs=21.4
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEe
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHW 30 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~ 30 (75)
+..+.+++|+.+++...=... .+-++-|
T Consensus 7 p~~~~v~~G~~v~l~C~~~G~-p~p~v~W 34 (98)
T cd05762 7 PEDMKVRAGESVELFCKVTGT-QPITCTW 34 (98)
T ss_pred CcCEEEECCCEEEEEEEEccc-CCCceEE
Confidence 456789999999998876655 5667777
No 223
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=28.80 E-value=36 Score=18.72 Aligned_cols=15 Identities=27% Similarity=0.162 Sum_probs=11.0
Q ss_pred cEEEecCCEEEEEEE
Q psy88 4 PKNVCEGDRVVVDVR 18 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~ 18 (75)
-+.++.||+|.|---
T Consensus 6 ~~~I~~GD~V~Vi~G 20 (83)
T CHL00141 6 KMHVKIGDTVKIISG 20 (83)
T ss_pred eCcccCCCEEEEeEc
Confidence 357889999987643
No 224
>PRK13855 type IV secretion system protein VirB10; Provisional
Probab=28.80 E-value=70 Score=22.69 Aligned_cols=21 Identities=24% Similarity=0.237 Sum_probs=18.6
Q ss_pred cccEEEecCCEEEEEEEeCCC
Q psy88 2 LYPKNVCEGDRVVVDVRNSMD 22 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~ 22 (75)
++||.+++|+.|.|-+.-.++
T Consensus 336 pPTl~i~qG~~V~I~VaRDLD 356 (376)
T PRK13855 336 PPTLKKNQGDTVSIFVARDLD 356 (376)
T ss_pred CCceEECCCCEEEEEECCCcc
Confidence 579999999999998887776
No 225
>PF08363 GbpC: Glucan-binding protein C; InterPro: IPR013574 This domain is found in glucan-binding protein C (GbpC) and in the V-region of surface protein antigen; both these proteins belong to the Spa family of Streptococcal proteins []. This domain consists of a beta-supersandwich of 18 beta-strands in two sheets. There are at least four types of glucan-binding proteins (Gbp) in Streptococcus mutans, GbpA, GbpB, GbpC and GbpD. These proteins promote the adhesion of Streptococcal bacteria to teeth and are associated with dental caries []. GbpC is a cell-wall anchoring protein that plays an important role in sucrose-dependent adhesion by binding to soluble glucan synthesised by glucosyltransferase D (GTFD) []. Spa antigens I/II are multi-functional proteins expressed at the cell wall surface of oral Streptococci, where they function as adhesins. Antigens I/II recognise a wide range of ligands. They exert an immunomodulatory effect on human cells and are important in inflammatory disorders, such as dental caries. These proteins can be divided into seven regions: signal peptide, N-terminal, A-region (alanine-rich), V-region (variable domain), P-region (proline-rich), C-terminal domain, and a cell wall anchor motif. The V-region is the central domain and exhibits the greatest variability in sequence, and is responsible for binding monocyte receptors, its binding stimulating the release of TNF-alpha from the monocytes. The crystal structure of the V-region revealed a lectin-like fold that displays a putative preformed carbohydrate-binding site stabilised by a metal ion [].; GO: 0005488 binding, 0009405 pathogenesis, 0044406 adhesion to host, 0009274 peptidoglycan-based cell wall; PDB: 1JMM_A 3IPK_A 3IOX_A 2WD6_B.
Probab=28.67 E-value=72 Score=21.58 Aligned_cols=17 Identities=24% Similarity=0.178 Sum_probs=12.6
Q ss_pred EEEecCCEEEEEEEeCC
Q psy88 5 KNVCEGDRVVVDVRNSM 21 (75)
Q Consensus 5 i~~~~Gd~v~i~~~N~~ 21 (75)
+.+++||+++++..|--
T Consensus 85 v~l~~G~~~tvTYtNL~ 101 (283)
T PF08363_consen 85 VLLKKGQTVTVTYTNLQ 101 (283)
T ss_dssp EEEETT-EEEEEEE--S
T ss_pred EEeccCCEEEEEEeCcc
Confidence 77999999999999974
No 226
>cd05899 IgV_TCR_beta Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) bet a chain. IgV_TCR_beta: immunoglobulin (Ig) variable domain of the beta chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta, polypeptide chains with variable (V) and constant (C) regions. This group includes the variable domain of the alpha chain of alpha/beta TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The variable domain of TCRs is responsible for antigen recognition, and is located at the N-terminus of the receptor. Gamma/delta TCRs recognize intact protein antigens; they recognize proteins antigens directly and without antigen processing, and MHC independently of the bound peptide.
Probab=28.61 E-value=1.1e+02 Score=16.75 Aligned_cols=27 Identities=11% Similarity=0.188 Sum_probs=19.8
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEe
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHW 30 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~ 30 (75)
+..+.+++|+.|.|.=.-... ...++|
T Consensus 5 p~~~~v~~G~~v~l~C~~~~~--~~~v~W 31 (110)
T cd05899 5 PRYLIKGRGQSVTLRCSQTSG--HDNMYW 31 (110)
T ss_pred CCceEEcCCCcEEEEEEECCC--CCEEEE
Confidence 446889999999998654433 457888
No 227
>TIGR01003 PTS_HPr_family Phosphotransferase System HPr (HPr) Family. The HPr family are bacterial proteins (or domains of proteins) which function in phosphoryl transfer system (PTS) systems. They include energy-coupling components which catalyze sugar uptake via a group translocation mechanism. The functions of most of these proteins are not known, but they presumably function in PTS-related regulatory capacities. All seed members are stand-alone HPr proteins, although the model also recognizes HPr domains of PTS fusion proteins. This family includes the related NPr protein.
Probab=28.42 E-value=32 Score=18.49 Aligned_cols=18 Identities=17% Similarity=0.191 Sum_probs=14.0
Q ss_pred ccEEEecCCEEEEEEEeC
Q psy88 3 YPKNVCEGDRVVVDVRNS 20 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N~ 20 (75)
+.|-++.||.++|...-.
T Consensus 51 l~Lg~~~G~~i~i~~~G~ 68 (82)
T TIGR01003 51 MMLGAGQGTEVTVSADGE 68 (82)
T ss_pred HhcCCCCCCEEEEEEeCc
Confidence 457789999999987543
No 228
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=28.33 E-value=56 Score=18.60 Aligned_cols=17 Identities=29% Similarity=0.243 Sum_probs=13.4
Q ss_pred cEEEecCCEEEEEEEeC
Q psy88 4 PKNVCEGDRVVVDVRNS 20 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~ 20 (75)
.|++++||.|.|.....
T Consensus 55 ~iwI~~GD~VlVsp~d~ 71 (99)
T TIGR00523 55 RIWIREGDVVIVKPWEF 71 (99)
T ss_pred cEEecCCCEEEEEEccC
Confidence 68899999999965443
No 229
>KOG1554|consensus
Probab=28.32 E-value=25 Score=24.17 Aligned_cols=8 Identities=25% Similarity=0.812 Sum_probs=6.1
Q ss_pred eeEEccCC
Q psy88 68 THFWHAHT 75 (75)
Q Consensus 68 t~~YH~H~ 75 (75)
.-|||+|.
T Consensus 134 VGWyHSHP 141 (347)
T KOG1554|consen 134 VGWYHSHP 141 (347)
T ss_pred eeeeecCC
Confidence 44999994
No 230
>PF00431 CUB: CUB domain CUB domain entry Spermadhesins family entry Link to schematic domain picture by Peer Bork. ; InterPro: IPR000859 The CUB domain (for complement C1r/C1s, Uegf, Bmp1) is a structural motif of approximately 110 residues found almost exclusively in extracellular and plasma membrane-associated proteins, many of which are developmentally regulated [, ]. These proteins are involved in a diverse range of functions, including complement activation, developmental patterning, tissue repair, axon guidance and angiogenesis, cell signalling, fertilisation, haemostasis, inflammation, neurotransmission, receptor-mediated endocytosis, and tumour suppression [, ]. Many CUB-containing proteins are peptidases belonging to MEROPS peptidase families M12A (astacin) and S1A (chymotrypsin). Proteins containing a CUB domain include: Mammalian complement subcomponents C1s/C1r, which form the calcium-dependent complex C1, the first component of the classical pathway of the complement system. Cricetidae sp. (Hamster) serine protease Casp, which degrades type I and IV collagen and fibronectin in the presence of calcium. Mammalian complement-activating component of Ra-reactive factor (RARF), a protease that cleaves the C4 component of complement. Vertebrate enteropeptidase (3.4.21.9 from EC), a type II membrane protein of the intestinal brush border, which activates trypsinogen. Vertebrate bone morphogenic protein 1 (BMP-1), a protein which induces cartilage and bone formation and expresses metalloendopeptidase activity. Sea urchin blastula proteins BP10 and SpAN. Caenorhabditis elegans hypothetical proteins F42A10.8 and R151.5. Neuropilin (A5 antigen), a calcium-independent cell adhesion molecule that functions during the formation of certain neuronal circuits. Fibropellins I and III from Strongylocentrotus purpuratus (Purple sea urchin). Mammalian hyaluronate-binding protein TSG-6 (or PS4), a serum and growth factor induced protein. Mammalian spermadhesins. Xenopus laevis embryonic protein UVS.2, which is expressed during dorsoanterior development. Several of the above proteins consist of a catalytic domain together with several CUB domains interspersed by calcium-binding EGF domains. Some CUB domains appear to be involved in oligomerisation and/or recognition of substrates and binding partners. For example, in the complement proteases, the CUB domains mediate dimerisation and binding to collagen-like regions of target proteins (e.g. C1q for C1r/C1s). The structure of CUB domains consists of a beta-sandwich with a jelly-roll fold. Almost all CUB domains contain four conserved cysteines that probably form two disulphide bridges (C1-C2, C3-C4). The CUB1 domains of C1s and Map19 have calcium-binding sites [].; PDB: 1SFP_A 3KQ4_B 2WNO_A 2QQK_A 2QQL_A 2QQO_B 2QQM_A 3POJ_A 3POB_A 3POG_B ....
Probab=28.29 E-value=60 Score=17.25 Aligned_cols=17 Identities=12% Similarity=0.112 Sum_probs=13.4
Q ss_pred cEEEecCCEEEEEEEeC
Q psy88 4 PKNVCEGDRVVVDVRNS 20 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~ 20 (75)
.|++..|..|+|+|.+-
T Consensus 30 ~i~~~~~~~I~l~f~~~ 46 (110)
T PF00431_consen 30 TITAPPGHRIRLTFLSF 46 (110)
T ss_dssp EEE-STTEEEEEEEEEE
T ss_pred EEEecccceeeeccccc
Confidence 68889999999999863
No 231
>COG2336 MazE Growth regulator [Signal transduction mechanisms]
Probab=28.16 E-value=32 Score=19.11 Aligned_cols=17 Identities=41% Similarity=0.513 Sum_probs=14.2
Q ss_pred cEEEecCCEEEEEEEeC
Q psy88 4 PKNVCEGDRVVVDVRNS 20 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~ 20 (75)
-|-++.||.|++.+.|.
T Consensus 23 ql~l~~g~~v~v~v~n~ 39 (82)
T COG2336 23 QLNLTIGDEVEVEVGND 39 (82)
T ss_pred HhCCCcCceEEEEEcCC
Confidence 35678999999999985
No 232
>cd00367 PTS-HPr_like Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation across the cell membrane. The phosphoryl group from phosphoenolpyruvate is transferred to HPr by enzyme I (EI). Phospho-HPr then transfers the phosphoryl group to one of several sugar-specific phosphoprotein intermediates. The conserved histidine in the N-terminus of HPr serves as an acceptor for the phosphoryl group of EI. In addition to the phosphotransferase proteins HPr and E1, this family also includes the closely related Carbon Catabolite Repressor (CCR) proteins which use the same phosphorylation mechanism and interact with transcriptional regulators to control expression of genes coding for utilization of less favored carbon sources.
Probab=28.11 E-value=35 Score=17.94 Aligned_cols=18 Identities=11% Similarity=0.292 Sum_probs=14.3
Q ss_pred ccEEEecCCEEEEEEEeC
Q psy88 3 YPKNVCEGDRVVVDVRNS 20 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N~ 20 (75)
+.|-++.||.++|.+...
T Consensus 47 ~~L~~~~G~~i~i~~~G~ 64 (77)
T cd00367 47 MSLGAKQGDEITLSAEGE 64 (77)
T ss_pred HHcCCCCCCEEEEEEECc
Confidence 457789999999988753
No 233
>PF00254 FKBP_C: FKBP-type peptidyl-prolyl cis-trans isomerase; InterPro: IPR001179 Synonym(s): Peptidylprolyl cis-trans isomerase FKBP-type peptidylprolyl isomerases (5.2.1.8 from EC) in vertebrates, are receptors for the two immunosuppressants, FK506 and rapamycin. The drugs inhibit T cell proliferation by arresting two distinct cytoplasmic signal transmission pathways. Peptidylprolyl isomerases accelerate protein folding by catalysing the cis-trans isomerisation of proline imidic peptide bonds in oligopeptides. These proteins are found in a variety of organisms.; GO: 0006457 protein folding; PDB: 1IX5_A 3JXV_A 3JYM_A 1T11_A 1PBK_A 1FD9_A 2VCD_A 3B7X_A 1Q6H_B 1Q6I_B ....
Probab=28.10 E-value=48 Score=17.65 Aligned_cols=15 Identities=27% Similarity=0.417 Sum_probs=11.9
Q ss_pred EecCCEEEEEEEeCC
Q psy88 7 VCEGDRVVVDVRNSM 21 (75)
Q Consensus 7 ~~~Gd~v~i~~~N~~ 21 (75)
++.||+|.|.+.=.+
T Consensus 5 ~~~gd~V~i~y~~~~ 19 (94)
T PF00254_consen 5 PKEGDTVTIHYTGRL 19 (94)
T ss_dssp BSTTSEEEEEEEEEE
T ss_pred CCCCCEEEEEEEEEE
Confidence 578999999887544
No 234
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=28.03 E-value=48 Score=19.51 Aligned_cols=14 Identities=36% Similarity=0.479 Sum_probs=11.7
Q ss_pred EEEecCCEEEEEEE
Q psy88 5 KNVCEGDRVVVDVR 18 (75)
Q Consensus 5 i~~~~Gd~v~i~~~ 18 (75)
..++.||+|+|.+.
T Consensus 17 p~f~~GD~V~V~~~ 30 (116)
T PRK05338 17 PEFRPGDTVRVHVK 30 (116)
T ss_pred CCcCCCCEEEEEEE
Confidence 36789999999886
No 235
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=27.99 E-value=58 Score=15.80 Aligned_cols=15 Identities=40% Similarity=0.290 Sum_probs=12.2
Q ss_pred EecCCEEEEEEEeCC
Q psy88 7 VCEGDRVVVDVRNSM 21 (75)
Q Consensus 7 ~~~Gd~v~i~~~N~~ 21 (75)
.+.||.+++.+.+..
T Consensus 45 ~~~Gd~v~v~i~~vd 59 (68)
T cd05685 45 VSVGDIVEVKVISID 59 (68)
T ss_pred cCCCCEEEEEEEEEE
Confidence 578999999987754
No 236
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=27.72 E-value=70 Score=15.62 Aligned_cols=14 Identities=36% Similarity=0.366 Sum_probs=11.7
Q ss_pred EecCCEEEEEEEeC
Q psy88 7 VCEGDRVVVDVRNS 20 (75)
Q Consensus 7 ~~~Gd~v~i~~~N~ 20 (75)
++.||.+++.+.+.
T Consensus 45 ~~~Gd~v~v~v~~~ 58 (68)
T cd04472 45 LKVGDEVKVKVIEV 58 (68)
T ss_pred cCCCCEEEEEEEEE
Confidence 58899999998765
No 237
>KOG4795|consensus
Probab=27.69 E-value=58 Score=21.82 Aligned_cols=19 Identities=11% Similarity=0.253 Sum_probs=16.1
Q ss_pred cEEEecCCEEEEEEEeCCC
Q psy88 4 PKNVCEGDRVVVDVRNSMD 22 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~ 22 (75)
.|.+.+|++|.|+|.|.-.
T Consensus 50 ~l~~~k~n~Vti~~~n~q~ 68 (264)
T KOG4795|consen 50 LLHKGKDNKVTIEFQNNQS 68 (264)
T ss_pred ceeecCCCeEEEEecCCCC
Confidence 3678899999999999865
No 238
>cd03693 EF1_alpha_II EF1_alpha_II: this family represents the domain II of elongation factor 1-alpha (EF-1a) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression.
Probab=27.43 E-value=57 Score=17.67 Aligned_cols=14 Identities=36% Similarity=0.546 Sum_probs=11.5
Q ss_pred EEecCCEEEEEEEe
Q psy88 6 NVCEGDRVVVDVRN 19 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N 19 (75)
.+..||.+.|.+.+
T Consensus 60 ~a~aG~~v~i~l~~ 73 (91)
T cd03693 60 EALPGDNVGFNVKN 73 (91)
T ss_pred EECCCCEEEEEECC
Confidence 47789999998876
No 239
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=27.43 E-value=52 Score=19.28 Aligned_cols=13 Identities=31% Similarity=0.391 Sum_probs=10.5
Q ss_pred cEEEecCCEEEEE
Q psy88 4 PKNVCEGDRVVVD 16 (75)
Q Consensus 4 ~i~~~~Gd~v~i~ 16 (75)
.+.++.||+|.|.
T Consensus 39 ~~~IkkGD~V~Vi 51 (114)
T TIGR01080 39 ALPVRKGDKVRIM 51 (114)
T ss_pred cceeecCCEEEEe
Confidence 4678999999885
No 240
>PRK10525 cytochrome o ubiquinol oxidase subunit II; Provisional
Probab=27.41 E-value=2.1e+02 Score=19.71 Aligned_cols=56 Identities=13% Similarity=-0.010 Sum_probs=36.3
Q ss_pred ccEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEcc
Q psy88 3 YPKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHA 73 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~ 73 (75)
..|.+-.|..|++.++-..- | |.+..+.. -| +.-.-||..-+..+. +++|+|.=.|
T Consensus 151 NeL~iP~g~pV~f~lTS~DV-----i--HSF~IP~L---g~-----K~damPG~~n~l~~~a~~~G~Y~G~C 207 (315)
T PRK10525 151 NEIAFPANVPVYFKVTSNSV-----M--NSFFIPRL---GS-----QIYAMAGMQTRLHLIANEPGTYDGIS 207 (315)
T ss_pred ccEEEecCCEEEEEEEEchh-----h--hhhhhhhh---CC-----eeecCCCceeEEEEEcCCCEEEEEEC
Confidence 46778888888888876532 2 44444321 11 222558888888888 8999887655
No 241
>PRK10850 PTS system phosphohistidinoprotein-hexose phosphotransferase subunit Hpr; Provisional
Probab=27.40 E-value=34 Score=18.70 Aligned_cols=17 Identities=12% Similarity=0.241 Sum_probs=13.6
Q ss_pred ccEEEecCCEEEEEEEe
Q psy88 3 YPKNVCEGDRVVVDVRN 19 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N 19 (75)
+.+-++.||.|+|...-
T Consensus 51 m~Lg~~~G~~v~i~~~G 67 (85)
T PRK10850 51 QTLGLTQGTVVTISAEG 67 (85)
T ss_pred HhcCCCCCCEEEEEEeC
Confidence 56778999999998654
No 242
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=27.02 E-value=51 Score=19.44 Aligned_cols=14 Identities=36% Similarity=0.427 Sum_probs=10.2
Q ss_pred EEecCCEEEEEEEe
Q psy88 6 NVCEGDRVVVDVRN 19 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N 19 (75)
..+.||+|++.++=
T Consensus 20 ~f~~GDtvrv~vki 33 (115)
T COG0335 20 SFRPGDTVRVHVKI 33 (115)
T ss_pred CCCCCCEEEEEEEE
Confidence 35679998877763
No 243
>COG4118 Phd Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]
Probab=26.96 E-value=24 Score=19.50 Aligned_cols=15 Identities=27% Similarity=0.534 Sum_probs=12.0
Q ss_pred EEecCCEEEEEEEeC
Q psy88 6 NVCEGDRVVVDVRNS 20 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~ 20 (75)
||+.|+.|.|+-.+.
T Consensus 20 rV~aGEev~IT~~G~ 34 (84)
T COG4118 20 RVRAGEEVIITKRGR 34 (84)
T ss_pred HHhCCCEEEEeeCCe
Confidence 678999999986654
No 244
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=26.91 E-value=86 Score=15.84 Aligned_cols=15 Identities=33% Similarity=0.233 Sum_probs=12.0
Q ss_pred EecCCEEEEEEEeCC
Q psy88 7 VCEGDRVVVDVRNSM 21 (75)
Q Consensus 7 ~~~Gd~v~i~~~N~~ 21 (75)
++.||.+++.+.+..
T Consensus 50 ~~~Gd~v~vkv~~~d 64 (76)
T cd04452 50 VKVGRKEVVKVIRVD 64 (76)
T ss_pred eCCCCEEEEEEEEEE
Confidence 588999999888643
No 245
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=26.81 E-value=66 Score=16.11 Aligned_cols=15 Identities=40% Similarity=0.246 Sum_probs=12.4
Q ss_pred EecCCEEEEEEEeCC
Q psy88 7 VCEGDRVVVDVRNSM 21 (75)
Q Consensus 7 ~~~Gd~v~i~~~N~~ 21 (75)
++.||.+++.+.+-.
T Consensus 45 ~~~Gd~i~~~i~~~~ 59 (70)
T cd05687 45 VKVGDEVEVYVLRVE 59 (70)
T ss_pred CCCCCEEEEEEEEEE
Confidence 678999999988754
No 246
>cd05860 Ig4_SCFR Fourth immunoglobulin (Ig)-like domain of stem cell factor receptor (SCFR). Ig4_SCFR: The fourth Immunoglobulin (Ig)-like domain in stem cell factor receptor (SCFR). SCFR is organized as an extracellular component having five IG-like domains, a transmembrane segment, and a cytoplasmic portion having protein tyrosine kinase activity. SCFR and its ligand SCF are critical for normal hematopoiesis, mast cell development, melanocytes and gametogenesis. SCF binds to the second and third Ig-like domains of SCFR. This fourth Ig-like domain participates in SCFR dimerization, which follows ligand binding. Deletion of this fourth domain abolishes the ligand-induced dimerization of SCFR and completely inhibits signal transduction.
Probab=26.73 E-value=95 Score=17.71 Aligned_cols=30 Identities=13% Similarity=0.057 Sum_probs=21.2
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEeC
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHWH 31 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~H 31 (75)
...+.|+.|+.+.+.+.=.+-..+..+-|.
T Consensus 10 ~~~~~v~~gE~~~L~V~ieAYP~p~~~~W~ 39 (101)
T cd05860 10 NTTIFVNAGENLDLIVEYEAYPKPEHQQWI 39 (101)
T ss_pred CceEEEECCCCEEEEEEEEeCCCCeeeEEE
Confidence 357899999999998875543134456775
No 247
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=26.64 E-value=47 Score=16.08 Aligned_cols=10 Identities=40% Similarity=0.395 Sum_probs=5.7
Q ss_pred EEEecCCEEE
Q psy88 5 KNVCEGDRVV 14 (75)
Q Consensus 5 i~~~~Gd~v~ 14 (75)
|.+++||.|+
T Consensus 16 v~V~~G~~Vk 25 (50)
T PF13533_consen 16 VYVKEGQQVK 25 (50)
T ss_pred EEecCCCEEc
Confidence 4566666653
No 248
>KOG1151|consensus
Probab=26.59 E-value=39 Score=25.15 Aligned_cols=21 Identities=24% Similarity=0.553 Sum_probs=13.7
Q ss_pred cCCCCEEE----EEEc-CCCeeeEEc
Q psy88 52 ITQGNTFR----YQFT-ANAGTHFWH 72 (75)
Q Consensus 52 i~pG~~~~----y~~~-~~~Gt~~YH 72 (75)
|.-++++. .+++ +-+|||||=
T Consensus 622 IMdddSy~~vdGmeLTSQgAGTYWYL 647 (775)
T KOG1151|consen 622 IMDDDSYNSVDGMELTSQGAGTYWYL 647 (775)
T ss_pred hccCCccCcccceeeecccCceeeec
Confidence 44455544 3556 779999994
No 249
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=26.58 E-value=86 Score=17.76 Aligned_cols=26 Identities=31% Similarity=0.306 Sum_probs=18.5
Q ss_pred cEEEecCCEEEEEEEeCCCCCCceEEeCCc
Q psy88 4 PKNVCEGDRVVVDVRNSMDGLENTIHWHGI 33 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~ 33 (75)
+.-+++||.|.|.+... ..++-.-|.
T Consensus 63 ~~~V~~G~~V~i~~~~~----~~~i~~~g~ 88 (122)
T TIGR03170 63 PWLVKRGDTVTVIARGG----GLSVTTEGK 88 (122)
T ss_pred ccEEcCCCEEEEEEecC----CEEEEEEEE
Confidence 45789999999998875 345544554
No 250
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=26.50 E-value=96 Score=15.87 Aligned_cols=16 Identities=31% Similarity=0.198 Sum_probs=12.5
Q ss_pred EEecCCEEEEEEEeCC
Q psy88 6 NVCEGDRVVVDVRNSM 21 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~~ 21 (75)
.++.||.|++.+..-.
T Consensus 57 ~~~~gd~v~v~v~~vd 72 (83)
T cd04471 57 VFRLGDKVKVRVVRVD 72 (83)
T ss_pred EEcCCCEEEEEEEEec
Confidence 4678999999887653
No 251
>MTH00076 COX2 cytochrome c oxidase subunit II; Provisional
Probab=26.46 E-value=1.9e+02 Score=18.78 Aligned_cols=55 Identities=11% Similarity=0.100 Sum_probs=33.4
Q ss_pred cEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEcc
Q psy88 4 PKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHA 73 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~ 73 (75)
.|.+-.|..+++.++-.. .| |+...+. -|.- . -.-||..-...+. +++|.|.--|
T Consensus 141 ~l~lP~~~~v~~~~tS~D-----Vi--Hsf~vP~----lg~k---~-da~PG~~n~~~~~~~~~G~~~g~C 196 (228)
T MTH00076 141 RMVVPMESPIRMLITAED-----VL--HSWAVPS----LGIK---T-DAIPGRLNQTSFIASRPGVYYGQC 196 (228)
T ss_pred eEEEecCCEEEEEEEecc-----cc--ccccccc----cCce---E-EccCCcceeEEEEeCCcEEEEEEC
Confidence 456666777777766542 22 5554442 2222 1 1447888887888 8899887666
No 252
>MTH00154 COX2 cytochrome c oxidase subunit II; Provisional
Probab=26.32 E-value=1.9e+02 Score=18.76 Aligned_cols=55 Identities=15% Similarity=0.180 Sum_probs=33.7
Q ss_pred cEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEcc
Q psy88 4 PKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHA 73 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~ 73 (75)
.|.+..|..+++.++-.. . | |+...+.. |.- .-.-||..-...+. +++|+|.--|
T Consensus 141 ~l~lP~~~~v~~~~tS~D--V---i--Hsf~vp~l----~~k----~davPG~~~~~~~~~~~~G~y~g~C 196 (227)
T MTH00154 141 RLVLPMNTQIRILITAAD--V---I--HSWTVPSL----GVK----VDAVPGRLNQLNFLINRPGLFFGQC 196 (227)
T ss_pred eEEEecCCEEEEEEEcCc--h---h--hheecccc----CCe----eecCCCceEEEEEEEcCceEEEEEe
Confidence 466777777777776542 1 2 44443321 111 12458888888888 8899887655
No 253
>PF07452 CHRD: CHRD domain; InterPro: IPR010895 CHRD (after SWISS-PROT abbreviation for chordin) is a novel domain identified in chordin, an inhibitor of bone morphogenetic proteins. This family includes bacterial homologues. It is anticipated to have an immunoglobulin-like beta-barrel structure based on limited similarity to superoxide dismutases but, as yet, no clear functional prediction can be made [].
Probab=26.27 E-value=1e+02 Score=17.30 Aligned_cols=18 Identities=11% Similarity=0.147 Sum_probs=12.4
Q ss_pred EEEEEeCCCCCCceEEeCC
Q psy88 14 VVDVRNSMDGLENTIHWHG 32 (75)
Q Consensus 14 ~i~~~N~~~~~~~~iH~HG 32 (75)
.|.+.|-.+ .++.+|+|+
T Consensus 38 ~i~~~gl~~-~~~~~hih~ 55 (119)
T PF07452_consen 38 SITLSGLSS-PPTAAHIHQ 55 (119)
T ss_pred EEEEeCCCC-CcEEEEEEc
Confidence 344455535 789999998
No 254
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=26.10 E-value=52 Score=17.42 Aligned_cols=16 Identities=31% Similarity=0.430 Sum_probs=11.9
Q ss_pred EEEecCCEEEEEEEeC
Q psy88 5 KNVCEGDRVVVDVRNS 20 (75)
Q Consensus 5 i~~~~Gd~v~i~~~N~ 20 (75)
+.++.||.|.|...+.
T Consensus 22 lgl~~Gd~v~v~~~~~ 37 (74)
T TIGR02609 22 LGLKEGDTLYVDEEEG 37 (74)
T ss_pred cCcCCCCEEEEEEECC
Confidence 4567889988877664
No 255
>PRK06518 hypothetical protein; Provisional
Probab=25.93 E-value=1.5e+02 Score=18.58 Aligned_cols=69 Identities=10% Similarity=0.101 Sum_probs=37.1
Q ss_pred cEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCC---CCCC--Cccc------ccccCCCCEEEEEEc-CCCeeeEE
Q psy88 4 PKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQY---SDGV--PFVT------QCPITQGNTFRYQFT-ANAGTHFW 71 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~---~DG~--~~~~------~~~i~pG~~~~y~~~-~~~Gt~~Y 71 (75)
+++|.-||+|+|.-.+........|-+.|++.+.... .+|. |.-. ...| .|+..+.... +..|....
T Consensus 27 ~v~V~DGDTl~l~~~~~~~~~~~~VRL~GIDAPE~~Q~c~~~~~~wp~G~~A~~~L~~li-~gk~V~~~~~~D~ygR~lA 105 (177)
T PRK06518 27 RAQVTSGVTFKLIADGWRKEITRDIRLYGVDTCAPRQKARLGDQEWPCGAVATAWLVTKT-LNKWLSCRQARMENGVHYA 105 (177)
T ss_pred eEEEEcCCEEEEeeccccCCCCeEEEEEEEcCCCCCCcccCCCCCCcHHHHHHHHHHHHH-CCCeEEEEEecccCCCEEE
Confidence 3578899999995221111125789999998764321 1121 1100 0112 4677766655 66666655
Q ss_pred cc
Q psy88 72 HA 73 (75)
Q Consensus 72 H~ 73 (75)
+|
T Consensus 106 ~~ 107 (177)
T PRK06518 106 QC 107 (177)
T ss_pred EE
Confidence 55
No 256
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=25.88 E-value=55 Score=18.92 Aligned_cols=15 Identities=33% Similarity=0.271 Sum_probs=10.7
Q ss_pred cEEEecCCEEEEEEE
Q psy88 4 PKNVCEGDRVVVDVR 18 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~ 18 (75)
.++++.||+|.|---
T Consensus 2 ~~~IrkGD~V~Vi~G 16 (104)
T COG0198 2 KMKVKKGDTVKVIAG 16 (104)
T ss_pred CcceecCCEEEEEec
Confidence 357788999887543
No 257
>smart00841 Elong-fact-P_C Elongation factor P, C-terminal. These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology PUBMED:15210970.
Probab=25.87 E-value=54 Score=16.76 Aligned_cols=13 Identities=46% Similarity=0.790 Sum_probs=9.5
Q ss_pred cEEEecCCEEEEE
Q psy88 4 PKNVCEGDRVVVD 16 (75)
Q Consensus 4 ~i~~~~Gd~v~i~ 16 (75)
++-+++||.|+|.
T Consensus 35 P~FI~~Gd~I~V~ 47 (56)
T smart00841 35 PLFINEGDKIKVD 47 (56)
T ss_pred CCcccCCCEEEEE
Confidence 3456889998885
No 258
>PF01557 FAA_hydrolase: Fumarylacetoacetate (FAA) hydrolase family Mutations in Swiss:P16930 cause inherited tyrosinemia type I.; InterPro: IPR002529 Fumarylacetoacetase (3.7.1.2 from EC; also known as fumarylacetoacetate hydrolase or FAH) catalyses the hydrolytic cleavage of a carbon-carbon bond in fumarylacetoacetate to yield fumarate and acetoacetate as the final step in phenylalanine and tyrosine degradation []. This is an essential metabolic function in humans, the lack of FAH causing type I tyrosinaemia, which is associated with liver and kidney abnormalities and neurological disorders [, ]. The enzyme mechanism involves a catalytic metal ion, a Glu/His catalytic dyad, and a charged oxyanion hole []. FAH folds into two domains: an N-terminal domain SH3-like beta-barrel, and a C-terminal with an unusual fold consisting of three layers of beta-sheet structures []. This entry represents the C-terminal domain of fumarylacetoacetase, as well as other domains that share a homologous sequence, including: 5-carboxymethyl-2-hydroxymuconate delta-isomerase (CHM isomerase; 5.3.3.10 from EC), which catalyses the conversion of 5-carboxymethyl-2-hydroxymuconate to 5-carboxy-2-oxohept-3-enedioate []. 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase (OPET decarboxylase; 4.1.1.68 from EC), which catalyses the conversion of 5-oxopent-3-ene-1,2,5-tricarboxylate to 2-oxohept-3-enedioate and carbon dioxide. Bifunctional enzyme HpcE (OPET decarboxylase 4.1.1.68 from EC/HHDD isomerase 5.3.3.10 from EC), which is a duplication consisting of a tandem repeat of two FAH C-terminal-like domains. This enzyme is responsible for the degradation of 4-hydroxyphenylacetate, a product of tyrosine and phenylalanine metabolism also released by lignin catabolism []. ; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1SAW_B 3LZK_B 3S52_B 2WQT_Q 1SV6_C 2DFU_B 1WZO_D 3QDF_A 1GTT_B 1I7O_C ....
Probab=25.73 E-value=91 Score=19.57 Aligned_cols=16 Identities=31% Similarity=0.457 Sum_probs=12.6
Q ss_pred cccEEEecCCEEEEEE
Q psy88 2 LYPKNVCEGDRVVVDV 17 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~ 17 (75)
...+.++.||+|++.+
T Consensus 191 ~~~~~l~~Gd~v~~~~ 206 (218)
T PF01557_consen 191 PPPVPLQPGDRVEAEI 206 (218)
T ss_dssp SCCEEEBTT-EEEEEE
T ss_pred cccccCCCCcEEEEEE
Confidence 3567899999999988
No 259
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=25.67 E-value=92 Score=14.92 Aligned_cols=16 Identities=31% Similarity=0.216 Sum_probs=13.0
Q ss_pred EEecCCEEEEEEEeCC
Q psy88 6 NVCEGDRVVVDVRNSM 21 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~~ 21 (75)
..+.||.+++.+..-.
T Consensus 46 ~~~~G~~v~~~V~~~~ 61 (72)
T smart00316 46 VLKVGDEVKVKVLSVD 61 (72)
T ss_pred eecCCCEEEEEEEEEe
Confidence 3788999999988754
No 260
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=25.51 E-value=39 Score=16.95 Aligned_cols=12 Identities=25% Similarity=0.515 Sum_probs=8.5
Q ss_pred EEEecCCEEEEE
Q psy88 5 KNVCEGDRVVVD 16 (75)
Q Consensus 5 i~~~~Gd~v~i~ 16 (75)
..++.||+|+|-
T Consensus 48 ~~L~~gD~vei~ 59 (65)
T PRK06944 48 RALAAGDRLDLV 59 (65)
T ss_pred ccCCCCCEEEEE
Confidence 356788888773
No 261
>CHL00010 infA translation initiation factor 1
Probab=25.42 E-value=76 Score=17.03 Aligned_cols=16 Identities=31% Similarity=0.457 Sum_probs=10.7
Q ss_pred EEEecCCEEEEEEEeC
Q psy88 5 KNVCEGDRVVVDVRNS 20 (75)
Q Consensus 5 i~~~~Gd~v~i~~~N~ 20 (75)
+++..||.|.+.+...
T Consensus 45 i~~~vGD~V~ve~~~~ 60 (78)
T CHL00010 45 IRILPGDRVKVELSPY 60 (78)
T ss_pred cccCCCCEEEEEEccc
Confidence 4566788888876443
No 262
>cd00174 SH3 Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
Probab=25.28 E-value=41 Score=15.37 Aligned_cols=15 Identities=20% Similarity=0.160 Sum_probs=11.1
Q ss_pred cEEEecCCEEEEEEE
Q psy88 4 PKNVCEGDRVVVDVR 18 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~ 18 (75)
.|.+++||.|.+.-.
T Consensus 15 ~l~~~~Gd~v~v~~~ 29 (54)
T cd00174 15 ELSFKKGDIIEVLEK 29 (54)
T ss_pred CCCCCCCCEEEEEEc
Confidence 466788999888644
No 263
>PF01345 DUF11: Domain of unknown function DUF11; InterPro: IPR001434 This group of sequences is represented by a conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis (Streptococcus faecalis), and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydia trachomatis outer membrane proteins. In C. trachomatis, three cysteine-rich proteins (also believed to be lipoproteins), MOMP, OMP6 and OMP3, make up the extracellular matrix of the outer membrane []. They are involved in the essential structural integrity of both the elementary body (EB) and recticulate body (RB) phase. They are thought to be involved in porin formation and, as these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism.; GO: 0005727 extrachromosomal circular DNA
Probab=25.25 E-value=60 Score=16.75 Aligned_cols=17 Identities=35% Similarity=0.661 Sum_probs=13.6
Q ss_pred ccCCCCEEEEEEc-CCCe
Q psy88 51 PITQGNTFRYQFT-ANAG 67 (75)
Q Consensus 51 ~i~pG~~~~y~~~-~~~G 67 (75)
.+.||+..+|.+. ...|
T Consensus 36 ~~~~Gd~v~ytitvtN~G 53 (76)
T PF01345_consen 36 TANPGDTVTYTITVTNTG 53 (76)
T ss_pred cccCCCEEEEEEEEEECC
Confidence 3789999999998 5544
No 264
>PRK10897 phosphohistidinoprotein-hexose phosphotransferase component of N-regulated PTS system (Npr); Provisional
Probab=25.18 E-value=37 Score=18.81 Aligned_cols=18 Identities=11% Similarity=0.265 Sum_probs=13.8
Q ss_pred ccEEEecCCEEEEEEEeC
Q psy88 3 YPKNVCEGDRVVVDVRNS 20 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N~ 20 (75)
+.|-++.||.|+|...=.
T Consensus 53 m~Lg~~~G~~i~v~~~G~ 70 (90)
T PRK10897 53 LMLDSAKGRQIEVEATGP 70 (90)
T ss_pred HHhCCCCCCEEEEEEECc
Confidence 467788999999987543
No 265
>PTZ00241 40S ribosomal protein S11; Provisional
Probab=25.08 E-value=37 Score=21.13 Aligned_cols=16 Identities=44% Similarity=0.331 Sum_probs=12.2
Q ss_pred cEEEecCCEEEEEEEe
Q psy88 4 PKNVCEGDRVVVDVRN 19 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N 19 (75)
.++++.||.|+|.=.-
T Consensus 114 ~~~~kvGD~V~I~EcR 129 (158)
T PTZ00241 114 CFDVKEGDIVVVGQCR 129 (158)
T ss_pred cCCCCCCCEEEEEEcC
Confidence 4678999999996433
No 266
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=25.05 E-value=93 Score=15.95 Aligned_cols=15 Identities=33% Similarity=0.317 Sum_probs=12.2
Q ss_pred EecCCEEEEEEEeCC
Q psy88 7 VCEGDRVVVDVRNSM 21 (75)
Q Consensus 7 ~~~Gd~v~i~~~N~~ 21 (75)
++.||++++.+....
T Consensus 49 ~~~Gd~v~vkv~~vd 63 (73)
T cd05686 49 VDVGEKVWVKVIGRE 63 (73)
T ss_pred ECCCCEEEEEEEEEC
Confidence 588999999987654
No 267
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=24.84 E-value=64 Score=19.16 Aligned_cols=15 Identities=33% Similarity=0.224 Sum_probs=11.4
Q ss_pred cEEEecCCEEEEEEE
Q psy88 4 PKNVCEGDRVVVDVR 18 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~ 18 (75)
.+.++.||.|.|.--
T Consensus 43 ~~~IkkGD~V~VisG 57 (120)
T PRK01191 43 SLPVRKGDTVKVMRG 57 (120)
T ss_pred cceEeCCCEEEEeec
Confidence 467889999988643
No 268
>PRK05863 sulfur carrier protein ThiS; Provisional
Probab=24.81 E-value=47 Score=16.99 Aligned_cols=10 Identities=30% Similarity=0.458 Sum_probs=7.3
Q ss_pred EecCCEEEEE
Q psy88 7 VCEGDRVVVD 16 (75)
Q Consensus 7 ~~~Gd~v~i~ 16 (75)
+++||+|+|-
T Consensus 50 L~~gD~ieIv 59 (65)
T PRK05863 50 LRDGARLEVV 59 (65)
T ss_pred cCCCCEEEEE
Confidence 5678888773
No 269
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=24.69 E-value=60 Score=16.98 Aligned_cols=16 Identities=19% Similarity=0.125 Sum_probs=13.6
Q ss_pred EecCCEEEEEEEeCCC
Q psy88 7 VCEGDRVVVDVRNSMD 22 (75)
Q Consensus 7 ~~~Gd~v~i~~~N~~~ 22 (75)
+++||.|.-.+.|-.+
T Consensus 1 ~k~G~~V~g~V~~i~~ 16 (74)
T cd05705 1 IKEGQLLRGYVSSVTK 16 (74)
T ss_pred CCCCCEEEEEEEEEeC
Confidence 3789999999999876
No 270
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=24.58 E-value=50 Score=16.48 Aligned_cols=15 Identities=13% Similarity=0.209 Sum_probs=10.4
Q ss_pred EEEecCCEEEEEEEe
Q psy88 5 KNVCEGDRVVVDVRN 19 (75)
Q Consensus 5 i~~~~Gd~v~i~~~N 19 (75)
+.+++||.|.+.++-
T Consensus 47 l~l~~G~~v~~~ik~ 61 (69)
T TIGR00638 47 LGLKPGKEVYAVIKA 61 (69)
T ss_pred CCCCCCCEEEEEEEC
Confidence 345688888887753
No 271
>TIGR01646 vgr_GE Rhs element Vgr protein. This model represents the Vgr family of proteins, associated with some classes of Rhs elements. This model does not include a large octapeptide repeat region, VGXXXXXX, found in the Vgr of Rhs classes G and E.
Probab=24.39 E-value=96 Score=22.01 Aligned_cols=24 Identities=13% Similarity=-0.003 Sum_probs=19.5
Q ss_pred EEEecCCEEEEEEEeCCCCCCceE
Q psy88 5 KNVCEGDRVVVDVRNSMDGLENTI 28 (75)
Q Consensus 5 i~~~~Gd~v~i~~~N~~~~~~~~i 28 (75)
+.-+.||+|.|.|.|..+++|..+
T Consensus 406 f~PrvG~EVlV~F~~GDpDrPvI~ 429 (483)
T TIGR01646 406 AIPRVGQEVIVGFLDGDPDRPIVT 429 (483)
T ss_pred ccCCCCCEEEEEEeCCCCCCCEEE
Confidence 445789999999999988777654
No 272
>TIGR01683 thiS thiamine biosynthesis protein ThiS. This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.
Probab=24.38 E-value=62 Score=16.33 Aligned_cols=12 Identities=33% Similarity=0.482 Sum_probs=8.6
Q ss_pred EEEecCCEEEEE
Q psy88 5 KNVCEGDRVVVD 16 (75)
Q Consensus 5 i~~~~Gd~v~i~ 16 (75)
..++.||+|.|-
T Consensus 47 ~~L~~gD~veii 58 (64)
T TIGR01683 47 TILKEGDRIEIV 58 (64)
T ss_pred eecCCCCEEEEE
Confidence 457788888763
No 273
>PF05489 Phage_tail_X: Phage Tail Protein X; InterPro: IPR008861 This entry is represented by Bacteriophage P2, GpX. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family is found in a family of phage tail proteins. Sequence analysis suggests that they are related to IPR002482 from INTERPRO which suggests a general peptidoglycan binding function.
Probab=24.35 E-value=35 Score=17.55 Aligned_cols=12 Identities=17% Similarity=0.224 Sum_probs=7.6
Q ss_pred ccEEEecCCEEE
Q psy88 3 YPKNVCEGDRVV 14 (75)
Q Consensus 3 ~~i~~~~Gd~v~ 14 (75)
++++.++||++.
T Consensus 1 m~v~t~~GDtlD 12 (60)
T PF05489_consen 1 MTVYTTQGDTLD 12 (60)
T ss_pred CEEEEeCcCcHH
Confidence 356667777754
No 274
>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein. ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.
Probab=24.34 E-value=62 Score=16.36 Aligned_cols=12 Identities=25% Similarity=0.520 Sum_probs=8.7
Q ss_pred EEEecCCEEEEE
Q psy88 5 KNVCEGDRVVVD 16 (75)
Q Consensus 5 i~~~~Gd~v~i~ 16 (75)
..++.||+|.|-
T Consensus 48 ~~L~~gD~V~ii 59 (65)
T cd00565 48 TPLQDGDRIEIV 59 (65)
T ss_pred eecCCCCEEEEE
Confidence 467888888763
No 275
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=24.28 E-value=61 Score=17.58 Aligned_cols=17 Identities=24% Similarity=0.266 Sum_probs=12.6
Q ss_pred EEecCCEEEEEEEeCCC
Q psy88 6 NVCEGDRVVVDVRNSMD 22 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~~~ 22 (75)
-++.||++.|.+.--.+
T Consensus 45 ~a~~Gd~V~vkI~~v~~ 61 (73)
T COG3269 45 GAEVGDEVKVKITKVKP 61 (73)
T ss_pred CCCCCCeeeEEEEEeec
Confidence 35789999998876543
No 276
>MTH00168 COX2 cytochrome c oxidase subunit II; Provisional
Probab=24.26 E-value=2.1e+02 Score=18.50 Aligned_cols=55 Identities=13% Similarity=0.163 Sum_probs=33.3
Q ss_pred cEEEecCCEEEEEEEeCCCCCCceEEeCCccccCCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEcc
Q psy88 4 PKNVCEGDRVVVDVRNSMDGLENTIHWHGIHQRGTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWHA 73 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~~~~~~~~iH~HG~~~~~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH~ 73 (75)
.+.+-.|..+++.++-.. .| |+...+.. |. ... .-||..-...+. +++|+|.--|
T Consensus 141 ~l~lP~~~~v~~~~tS~D-----Vi--Hsf~vP~l----g~---k~d-aiPG~~n~~~~~~~~~G~~~g~C 196 (225)
T MTH00168 141 RLVLPMDSKIRVLVTSAD-----VL--HSWTLPSL----GL---KMD-AVPGRLNQLAFLSSRPGSFYGQC 196 (225)
T ss_pred eEEEecCCEEEEEEEeCC-----hh--hccccccc----cc---ccc-CCCCeEEEEEEEcCCCEEEEEEc
Confidence 456666777777766553 12 44443321 11 111 348888888888 8999987766
No 277
>PF06205 GT36_AF: Glycosyltransferase 36 associated family ; InterPro: IPR010403 This domain is found in the NvdB protein (P20471 from SWISSPROT), which is involved in the production of beta-(1-->2)-glucan.; PDB: 1V7V_A 1V7W_A 1V7X_A 3ACT_B 2CQT_A 3QFY_B 3QFZ_A 2CQS_A 3QG0_B 3AFJ_A ....
Probab=24.11 E-value=1.1e+02 Score=16.76 Aligned_cols=16 Identities=13% Similarity=-0.045 Sum_probs=11.1
Q ss_pred cEEEecCCEEEEEEEe
Q psy88 4 PKNVCEGDRVVVDVRN 19 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N 19 (75)
.|+++.|++.+|.|.-
T Consensus 67 ~v~L~PGe~~~v~f~l 82 (90)
T PF06205_consen 67 RVTLEPGEEKEVVFLL 82 (90)
T ss_dssp EEEE-TT-EEEEEEEE
T ss_pred EEEECCCCEEEEEEEE
Confidence 4788999999998753
No 278
>cd05716 Ig_pIgR Immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR). Ig_pIgR: Immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR). pIgR delivers dimeric IgA and pentameric IgM to mucosal secretions. Polymeric immunoglobulin (pIgs) are the first defense against pathogens and toxins. IgA and IgM can form polymers via an 18-residue extension at their c-termini referred to as the tailpiece. pIgR transports pIgs across mucosal epithelia into mucosal secretions. Human pIgR is a glycosylated type I transmembrane protein, comprised of a 620 residue extracellular region, a 23 residue transmembrane region, and a 103 residue cytoplasmic tail. The extracellular region contains five domains that share sequence similarity with Ig variable (v) regions.
Probab=24.04 E-value=88 Score=16.65 Aligned_cols=14 Identities=14% Similarity=0.007 Sum_probs=11.5
Q ss_pred cEEEecCCEEEEEE
Q psy88 4 PKNVCEGDRVVVDV 17 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~ 17 (75)
++.+.+|+.|.|.=
T Consensus 1 ~v~~~~G~~vtl~C 14 (98)
T cd05716 1 VVTGELGGSVTIPC 14 (98)
T ss_pred CEEEEeCCeEEEEe
Confidence 46789999999974
No 279
>PRK13831 conjugal transfer protein TrbI; Provisional
Probab=24.01 E-value=99 Score=22.37 Aligned_cols=21 Identities=14% Similarity=0.039 Sum_probs=18.1
Q ss_pred cccEEEecCCEEEEEEEeCCC
Q psy88 2 LYPKNVCEGDRVVVDVRNSMD 22 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~ 22 (75)
++||.+++|..|.|-+.-.+.
T Consensus 406 ~PTitirpG~~v~I~V~RDL~ 426 (432)
T PRK13831 406 QPTLEIRPGYKFNVLVDQDIV 426 (432)
T ss_pred CCceEeCCCCEEEEEeccCcc
Confidence 579999999999998877665
No 280
>PRK13881 conjugal transfer protein TrbI; Provisional
Probab=23.95 E-value=86 Score=22.93 Aligned_cols=21 Identities=24% Similarity=0.158 Sum_probs=18.6
Q ss_pred cccEEEecCCEEEEEEEeCCC
Q psy88 2 LYPKNVCEGDRVVVDVRNSMD 22 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~ 22 (75)
++||++++|+++.|-|...++
T Consensus 442 pPTItI~qG~rinIiVaRDLd 462 (472)
T PRK13881 442 APTLEIRPGYRFNVIVTKDMT 462 (472)
T ss_pred CCceEECCCCEEEEEecCccc
Confidence 579999999999999888776
No 281
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=23.87 E-value=71 Score=17.70 Aligned_cols=14 Identities=36% Similarity=0.347 Sum_probs=11.0
Q ss_pred EEecCCEEEEEEEe
Q psy88 6 NVCEGDRVVVDVRN 19 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N 19 (75)
.+++||.|+|.|.=
T Consensus 52 ~~~~Gd~V~Vsf~i 65 (84)
T PF11325_consen 52 NFQVGDEVKVSFNI 65 (84)
T ss_pred cCCCCCEEEEEEEe
Confidence 56789999998753
No 282
>cd03697 EFTU_II EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the catalytic or G-domain. The G-domain is composed of about 200 amino acid residues, arranged into a predominantly parallel six-stranded beta-sheet core surrounded by seven a-helices. Non-catalytic domains II and III are beta-barrels of seven and six, respectively, antiparallel beta-strands that share an extended interface. Either non-catalytic domain is composed of about 100 amino acid residues. EF-Tu proteins exist in two principal conformations: in a compact one, EF-Tu*GTP, with tight interfaces between all three domains and a high affinity for aminoacyl-tRNA, and in an open one, EF-Tu*GDP, with essentially no G-domain-domain II interactions and a low affinity for aminoacyl-tRNA. EF-Tu has approximately a 100-fold higher
Probab=23.77 E-value=77 Score=16.95 Aligned_cols=14 Identities=36% Similarity=0.382 Sum_probs=10.6
Q ss_pred EEecCCEEEEEEEe
Q psy88 6 NVCEGDRVVVDVRN 19 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N 19 (75)
.+..||.+.+.|++
T Consensus 58 ~a~~G~~v~l~l~~ 71 (87)
T cd03697 58 EAEAGDNVGVLLRG 71 (87)
T ss_pred EECCCCEEEEEECC
Confidence 46678888888865
No 283
>PF03712 Cu2_monoox_C: Copper type II ascorbate-dependent monooxygenase, C-terminal domain; PDB: 1YI9_A 3MLL_A 1SDW_A 3MID_A 1YIP_A 3PHM_A 3MIC_A 3MIB_A 1OPM_A 3MIG_A ....
Probab=23.69 E-value=74 Score=19.26 Aligned_cols=16 Identities=19% Similarity=0.347 Sum_probs=11.3
Q ss_pred ccEEEecCCEEEEEEE
Q psy88 3 YPKNVCEGDRVVVDVR 18 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~ 18 (75)
.++.++.||.|+++-.
T Consensus 85 ~~v~i~~GD~l~~~C~ 100 (156)
T PF03712_consen 85 EPVTIPPGDTLRTECT 100 (156)
T ss_dssp EEEEE-TT-EEEEEEE
T ss_pred CceEecCCCEEEEEEE
Confidence 4689999999998755
No 284
>COG2847 Copper(I)-binding protein [Inorganic ion transport and metabolism]
Probab=23.56 E-value=59 Score=20.05 Aligned_cols=15 Identities=40% Similarity=0.618 Sum_probs=9.8
Q ss_pred cEEEecCCEEEEEEE
Q psy88 4 PKNVCEGDRVVVDVR 18 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~ 18 (75)
.-.+++||+|.++|+
T Consensus 113 K~pl~eGd~v~vtL~ 127 (151)
T COG2847 113 KKPLKEGDKVPVTLK 127 (151)
T ss_pred CCCccCCCEEEEEEE
Confidence 334567777777665
No 285
>PF09347 DUF1989: Domain of unknown function (DUF1989); InterPro: IPR018959 This entry represents proteins that are functionally uncharacterised. ; PDB: 3ORU_A 3SIY_C 3DI4_A.
Probab=23.53 E-value=79 Score=19.57 Aligned_cols=13 Identities=15% Similarity=0.174 Sum_probs=8.0
Q ss_pred cEEEecCCEEEEE
Q psy88 4 PKNVCEGDRVVVD 16 (75)
Q Consensus 4 ~i~~~~Gd~v~i~ 16 (75)
..++++|+.++|.
T Consensus 11 a~~v~rG~~lri~ 23 (166)
T PF09347_consen 11 AFRVKRGQVLRIT 23 (166)
T ss_dssp EEEE-TT-EEEEE
T ss_pred EEEECCCCEEEEE
Confidence 4678899987765
No 286
>PF10610 Tafi-CsgC: Thin aggregative fimbriae synthesis protein; InterPro: IPR014491 Thin aggressive fibres known as curli fibres or fimbriae (curli; Tafi) are cell-surface protein polymers found in Salmonella typhimurium and Escherichia coli that mediate interactions important for host and environmental persistence, development of biofilms, motility, colonisation and invasion of cells, and conjugation []. Four general assembly pathways for different fimbriae have been proposed, one of which is extracellular nucleation-precipitation (ENP), which differs from the others in that fibre-growth occurs extracellularly. Thin aggregative fimbriae are the only fimbriae dependent on the ENP pathway. Tafi were first identified in Salmonella spp and the controlling operon termed agf; however subsequent isolation of the homologous operon in E coli led to its being called csg. Tafi are known as curli because, in the absence of extracellular polysaccharides, their morphology appears curled; however, when expressed with such polysaccharides their morphology appears as a tangled amorphous matrix. The gene agfC is found to be transcribed at low levels, localised to the periplasm in a mature form, and in combination with AgfE is important for AgfA extracellular assembly, which facilitates the synthesis of Tafi. The genes involved in Tafi production are organised into two adjacent divergently transcribed operons, agfBAC and agfDEFG, both of which are required for biosynthesis and assembly [].; PDB: 2XSK_A 2Y2T_A 2Y2Y_A.
Probab=23.51 E-value=93 Score=18.09 Aligned_cols=18 Identities=33% Similarity=0.405 Sum_probs=11.2
Q ss_pred ccEEEecCCEEEEEEEeC
Q psy88 3 YPKNVCEGDRVVVDVRNS 20 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N~ 20 (75)
+-+.+..||+|.|.+.=.
T Consensus 71 ls~ni~p~D~v~I~VtvS 88 (106)
T PF10610_consen 71 LSFNISPGDKVKIIVTVS 88 (106)
T ss_dssp EEEE--TT-EEEEEEEEE
T ss_pred EEEEeCCCCeEEEEEEEc
Confidence 346778899999988744
No 287
>TIGR00046 RNA methyltransferase, RsmE family. Members of this protein family, previously called conserved hypothetical protein TIGR00046, include the YggJ protein of E. coli, which has now been shown to methylate U1498 in 16S rRNA.
Probab=23.36 E-value=44 Score=21.61 Aligned_cols=14 Identities=14% Similarity=0.135 Sum_probs=11.5
Q ss_pred cEEEecCCEEEEEE
Q psy88 4 PKNVCEGDRVVVDV 17 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~ 17 (75)
.+|+++||.|+|.-
T Consensus 29 VlR~~~Gd~v~v~~ 42 (240)
T TIGR00046 29 VLRLKKGDKLKLLD 42 (240)
T ss_pred cccCCCCCEEEEEe
Confidence 67999999988753
No 288
>TIGR03361 VI_Rhs_Vgr type VI secretion system Vgr family protein. Members of this protein family belong to the Rhs element Vgr protein family (see TIGR01646), but furthermore all are found in genomes with type VI secretion loci. However, members of this protein family, although recognizably correlated to type VI secretion according the partial phylogenetic profiling algorithm, are often found far the type VI secretion locus.
Probab=23.34 E-value=96 Score=22.22 Aligned_cols=23 Identities=22% Similarity=0.055 Sum_probs=18.7
Q ss_pred EEecCCEEEEEEEeCCCCCCceE
Q psy88 6 NVCEGDRVVVDVRNSMDGLENTI 28 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~~~~~~~~i 28 (75)
.-+.||+|.|.|.|..+.+|..+
T Consensus 418 ~PrvG~EVlV~F~~GDpdrPvI~ 440 (513)
T TIGR03361 418 IPRVGQEVVVDFLEGDPDRPIVT 440 (513)
T ss_pred CCCCCCEEEEEEcCCCCCCCEEE
Confidence 34789999999999988777654
No 289
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=23.33 E-value=37 Score=20.69 Aligned_cols=16 Identities=13% Similarity=0.403 Sum_probs=11.6
Q ss_pred EEEecCCEEEEEEEeC
Q psy88 5 KNVCEGDRVVVDVRNS 20 (75)
Q Consensus 5 i~~~~Gd~v~i~~~N~ 20 (75)
+.++.||.|+|.+..+
T Consensus 57 ~~~~vGD~V~v~i~e~ 72 (154)
T PRK10862 57 QPLVPGQKVELGIAEG 72 (154)
T ss_pred CCCCCCCEEEEecchh
Confidence 3467788888877654
No 290
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=23.28 E-value=88 Score=15.11 Aligned_cols=14 Identities=43% Similarity=0.536 Sum_probs=11.3
Q ss_pred EecCCEEEEEEEeC
Q psy88 7 VCEGDRVVVDVRNS 20 (75)
Q Consensus 7 ~~~Gd~v~i~~~N~ 20 (75)
++.||.+++.+...
T Consensus 45 ~~~Gd~v~v~v~~~ 58 (69)
T cd05692 45 LKEGDKVKVKVLSI 58 (69)
T ss_pred cCCCCEEEEEEEEE
Confidence 57899999988764
No 291
>PRK01777 hypothetical protein; Validated
Probab=23.27 E-value=46 Score=18.72 Aligned_cols=11 Identities=36% Similarity=0.543 Sum_probs=8.7
Q ss_pred EEecCCEEEEE
Q psy88 6 NVCEGDRVVVD 16 (75)
Q Consensus 6 ~~~~Gd~v~i~ 16 (75)
.++.||+|+|-
T Consensus 64 ~L~dGDRVeIy 74 (95)
T PRK01777 64 VLRDGDRVEIY 74 (95)
T ss_pred cCCCCCEEEEe
Confidence 46789999884
No 292
>PF09285 Elong-fact-P_C: Elongation factor P, C-terminal; InterPro: IPR015365 These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology []. ; GO: 0043043 peptide biosynthetic process, 0005737 cytoplasm; PDB: 1YBY_A 3OYY_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H.
Probab=23.18 E-value=64 Score=16.49 Aligned_cols=11 Identities=45% Similarity=0.730 Sum_probs=6.3
Q ss_pred EEecCCEEEEE
Q psy88 6 NVCEGDRVVVD 16 (75)
Q Consensus 6 ~~~~Gd~v~i~ 16 (75)
-+++||.|+|.
T Consensus 37 FI~~Gd~I~Vd 47 (56)
T PF09285_consen 37 FIEEGDKIKVD 47 (56)
T ss_dssp T--TT-EEEEE
T ss_pred eecCCCEEEEE
Confidence 35789999885
No 293
>PF11797 DUF3324: Protein of unknown function C-terminal (DUF3324); InterPro: IPR021759 This family consists of several hypothetical bacterial proteins of unknown function.
Probab=23.15 E-value=1e+02 Score=18.25 Aligned_cols=22 Identities=9% Similarity=0.329 Sum_probs=17.0
Q ss_pred ccCCCCEEEEEEc-C----CCeeeEEc
Q psy88 51 PITQGNTFRYQFT-A----NAGTHFWH 72 (75)
Q Consensus 51 ~i~pG~~~~y~~~-~----~~Gt~~YH 72 (75)
-++|...|.|.+. + .||+|-++
T Consensus 85 ~mAPNS~f~~~i~~~~~~lk~G~Y~l~ 111 (140)
T PF11797_consen 85 QMAPNSNFNFPIPLGGKKLKPGKYTLK 111 (140)
T ss_pred EECCCCeEEeEecCCCcCccCCEEEEE
Confidence 3789999999888 2 58888665
No 294
>PRK09798 antitoxin MazE; Provisional
Probab=23.03 E-value=61 Score=17.72 Aligned_cols=16 Identities=25% Similarity=0.337 Sum_probs=11.5
Q ss_pred EEEecCCEEEEEEEeC
Q psy88 5 KNVCEGDRVVVDVRNS 20 (75)
Q Consensus 5 i~~~~Gd~v~i~~~N~ 20 (75)
+.++.||.|+|.+.|.
T Consensus 25 l~l~~g~~vei~v~~~ 40 (82)
T PRK09798 25 LNLNIDDEVKIDLVDG 40 (82)
T ss_pred cCCCCCCEEEEEEECC
Confidence 3456788888888764
No 295
>COG1596 Wza Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]
Probab=22.90 E-value=92 Score=20.25 Aligned_cols=19 Identities=16% Similarity=0.141 Sum_probs=15.4
Q ss_pred ccEEEecCCEEEEEEEeCC
Q psy88 3 YPKNVCEGDRVVVDVRNSM 21 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N~~ 21 (75)
...++..||.|+|++.=.-
T Consensus 44 ~~y~lg~GD~l~I~v~e~~ 62 (239)
T COG1596 44 SAYRLGPGDVLRITVFEAP 62 (239)
T ss_pred CceeecCCCEEEEEecccC
Confidence 4578899999999987553
No 296
>cd05752 Ig1_FcgammaR_like Frst immunoglobulin (Ig)-like domain of Fcgamma-receptors (FcgammaRs) and similar proteins. Ig1_FcgammaR_like: domain similar to the first immunoglobulin (Ig)-like domain of Fcgamma-receptors (FcgammaRs). Interactions between IgG and FcgammaR are important to the initiation of cellular and humoral response. IgG binding to FcgammaR leads to a cascade of signals and ultimately to functions such as antibody-dependent-cellular-cytotoxicity (ADCC), endocytosis, phagocytosis, release of inflammatory mediators, etc. FcgammaR has two Ig-like domains. This group also contains FcepsilonRI, which binds IgE with high affinity.
Probab=22.79 E-value=90 Score=16.33 Aligned_cols=29 Identities=14% Similarity=0.289 Sum_probs=17.8
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEe
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHW 30 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~ 30 (75)
+....+.+||.|.++=.=.....+..+.|
T Consensus 7 P~~~~v~~G~~V~L~C~~~~~p~~~~~~W 35 (78)
T cd05752 7 PPWTTIFQGEKVTLTCNGFNSPEQNSTQW 35 (78)
T ss_pred CCCeEeeCCCCEEEEEeCCCCCCCccEEE
Confidence 34468899999998876332212334555
No 297
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=22.71 E-value=95 Score=15.44 Aligned_cols=15 Identities=27% Similarity=0.266 Sum_probs=12.2
Q ss_pred EecCCEEEEEEEeCC
Q psy88 7 VCEGDRVVVDVRNSM 21 (75)
Q Consensus 7 ~~~Gd~v~i~~~N~~ 21 (75)
++.||.+++.+.+-.
T Consensus 45 ~~~Gd~v~~~v~~~d 59 (73)
T cd05691 45 FKVGDEVEAKITNVD 59 (73)
T ss_pred cCCCCEEEEEEEEEe
Confidence 578999999888754
No 298
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=22.58 E-value=93 Score=15.69 Aligned_cols=15 Identities=20% Similarity=-0.051 Sum_probs=12.3
Q ss_pred EecCCEEEEEEEeCC
Q psy88 7 VCEGDRVVVDVRNSM 21 (75)
Q Consensus 7 ~~~Gd~v~i~~~N~~ 21 (75)
.+.||.+++.+.+..
T Consensus 48 ~~~Gd~v~~~V~~~d 62 (73)
T cd05706 48 FKKNDIVRACVLSVD 62 (73)
T ss_pred cCCCCEEEEEEEEEe
Confidence 578999999988754
No 299
>TIGR03027 pepcterm_export putative polysaccharide export protein, PEP-CTERM sytem-associated. This protein family belongs to the larger set of polysaccharide biosynthesis/export proteins described by Pfam model pfam02563. Members of this family are variable in either containing of lacking a 78-residue insert, but appear to fall within a single clade, nevertheless, where the regions in which the gene is found encode components of the PEP-CTERM/EpsH proposed exosortase protein sorting system.
Probab=22.42 E-value=69 Score=19.38 Aligned_cols=17 Identities=18% Similarity=0.348 Sum_probs=14.0
Q ss_pred EEecCCEEEEEEEeCCC
Q psy88 6 NVCEGDRVVVDVRNSMD 22 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~~~ 22 (75)
++..||.+.|.+....+
T Consensus 2 ~l~pGD~l~i~v~~~~~ 18 (165)
T TIGR03027 2 VIGPGDSLNINVWRNPE 18 (165)
T ss_pred CcCCCCEEEEEEcCCcc
Confidence 46789999999998643
No 300
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=22.23 E-value=56 Score=16.67 Aligned_cols=12 Identities=25% Similarity=0.459 Sum_probs=8.5
Q ss_pred EEEecCCEEEEE
Q psy88 5 KNVCEGDRVVVD 16 (75)
Q Consensus 5 i~~~~Gd~v~i~ 16 (75)
..+++||+|+|-
T Consensus 49 ~~L~~gD~Ieii 60 (66)
T PRK08053 49 HIVQDGDQILLF 60 (66)
T ss_pred cccCCCCEEEEE
Confidence 457788888763
No 301
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=22.23 E-value=96 Score=15.45 Aligned_cols=16 Identities=13% Similarity=-0.078 Sum_probs=12.7
Q ss_pred EecCCEEEEEEEeCCC
Q psy88 7 VCEGDRVVVDVRNSMD 22 (75)
Q Consensus 7 ~~~Gd~v~i~~~N~~~ 22 (75)
++.||.+++.+.+...
T Consensus 45 ~~~Gd~v~~~v~~~d~ 60 (68)
T cd05707 45 FKVGQLVKGKIVSIDP 60 (68)
T ss_pred cCCCCEEEEEEEEEeC
Confidence 5789999999887643
No 302
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=22.19 E-value=59 Score=17.39 Aligned_cols=11 Identities=45% Similarity=0.549 Sum_probs=8.8
Q ss_pred EEecCCEEEEE
Q psy88 6 NVCEGDRVVVD 16 (75)
Q Consensus 6 ~~~~Gd~v~i~ 16 (75)
.++.||.|+|+
T Consensus 44 ~~~~Gd~V~vt 54 (78)
T cd04486 44 DVAVGDLVRVT 54 (78)
T ss_pred CCCCCCEEEEE
Confidence 45789999986
No 303
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=22.14 E-value=93 Score=15.94 Aligned_cols=16 Identities=6% Similarity=-0.062 Sum_probs=12.7
Q ss_pred EecCCEEEEEEEeCCC
Q psy88 7 VCEGDRVVVDVRNSMD 22 (75)
Q Consensus 7 ~~~Gd~v~i~~~N~~~ 22 (75)
++.||.+++.+.+-..
T Consensus 47 ~~vG~~v~~kV~~id~ 62 (71)
T cd05696 47 FKAGTTHKARIIGYSP 62 (71)
T ss_pred cCCCCEEEEEEEEEeC
Confidence 6789999999886543
No 304
>cd05754 Ig3_Perlecan_like Third immunoglobulin (Ig)-like domain found in Perlecan and similar proteins. Ig3_Perlecan_like: domain similar to the third immunoglobulin (Ig)-like domain found in Perlecan. Perlecan is a large multi-domain heparin sulfate proteoglycan, important in tissue development and organogenesis. Perlecan can be represented as 5 major portions; its fourth major portion (domain IV) is a tandem repeat of immunoglobulin-like domains (Ig2-Ig15), which can vary in size due to alternative splicing. Perlecan binds many cellular and extracellular ligands. Its domain IV region has many binding sites. Some of these have been mapped at the level of individual Ig-like domains, including a site restricted to the Ig5 domain for heparin/sulfatide, a site restricted to the Ig3 domain for nidogen-1 and nidogen-2, a site restricted to Ig4-5 for fibronectin, and sites restricted to Ig2 and to Ig13-15 for fibulin-2.
Probab=22.13 E-value=1.3e+02 Score=15.46 Aligned_cols=29 Identities=21% Similarity=0.254 Sum_probs=19.4
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEe
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHW 30 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~ 30 (75)
+..+.+.+|+.+++.=.-........+.|
T Consensus 8 p~~~~v~~G~~v~L~C~~~~~~~~~~i~W 36 (85)
T cd05754 8 PRSQEVRPGADVSFICRAKSKSPAYTLVW 36 (85)
T ss_pred CCceEEcCCCCEEEEEEcCCCCCCcEEEE
Confidence 45678899999998876432213456777
No 305
>PF12790 T6SS-SciN: Type VI secretion lipoprotein; InterPro: IPR017734 This entry represents a family of lipoproteins associated with IAHP-related loci, thought to be type VI secretion system protein []. ; PDB: 3RX9_A.
Probab=22.03 E-value=92 Score=18.39 Aligned_cols=17 Identities=6% Similarity=0.161 Sum_probs=11.2
Q ss_pred ccccCCCCEEEEEEc-CC
Q psy88 49 QCPITQGNTFRYQFT-AN 65 (75)
Q Consensus 49 ~~~i~pG~~~~y~~~-~~ 65 (75)
+.-+.||++.++.+. +.
T Consensus 82 e~~l~Pg~~~~~~~~~~~ 99 (142)
T PF12790_consen 82 EFVLQPGESRTLTLDRDP 99 (142)
T ss_dssp EEEE-TT-EEEEEEE--T
T ss_pred EEEECCCCcEeeeEccCC
Confidence 344899999999998 44
No 306
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=21.96 E-value=99 Score=16.06 Aligned_cols=60 Identities=13% Similarity=0.293 Sum_probs=26.8
Q ss_pred EecCCEEEEEEEeCCCCCC--ceEEeCCcccc-----CCCCCCCCCcccccccCCCCEEEEEEc-CCCeeeEEc
Q psy88 7 VCEGDRVVVDVRNSMDGLE--NTIHWHGIHQR-----GTQYSDGVPFVTQCPITQGNTFRYQFT-ANAGTHFWH 72 (75)
Q Consensus 7 ~~~Gd~v~i~~~N~~~~~~--~~iH~HG~~~~-----~~~~~DG~~~~~~~~i~pG~~~~y~~~-~~~Gt~~YH 72 (75)
++.|+.|+|.+.|... .. ..--..|.... ..|..+|. ..++..|+.....+. +.. .|-+-
T Consensus 1 L~iG~~i~i~i~~~~~-~~~~y~S~v~g~~~~~~l~i~~P~~~g~----~~~l~~g~~v~v~~~~~~~-~y~F~ 68 (87)
T PF12945_consen 1 LKIGQKIEIEITNPTG-EKGRYKSRVIGIDDDRYLIISMPMEKGR----PIPLREGEEVIVRFISEDG-VYAFK 68 (87)
T ss_dssp --TT-EEEEEEE-TTS--EEEEEEEEEEEETTTEEEEE---CCHH----HCCS-TT-EEEEEEEE-SC-EEEEE
T ss_pred CCCCCEEEEEEECCCC-ceEEEEEEEEEECCCCEEEEEcCccCCc----EEeecCCCEEEEEEEECCe-EEEEE
Confidence 3679999999987763 22 22233333221 01112222 234778888888887 332 55443
No 307
>PF13157 DUF3992: Protein of unknown function (DUF3992)
Probab=21.91 E-value=77 Score=17.88 Aligned_cols=13 Identities=15% Similarity=0.424 Sum_probs=11.6
Q ss_pred ccCCCCEEEEEEc
Q psy88 51 PITQGNTFRYQFT 63 (75)
Q Consensus 51 ~i~pG~~~~y~~~ 63 (75)
-++||++..|.++
T Consensus 57 tV~pG~S~S~T~~ 69 (92)
T PF13157_consen 57 TVQPGNSRSFTVR 69 (92)
T ss_pred EECCCceEEEEec
Confidence 4899999999987
No 308
>cd09219 TLP-F thaumatin-like proteins: basidiomycete homologs. This subfamily is represented by Lentinula edodes TLG1, a thaumatin-like protein (TLP), as well as, other basidiomycete homologs. In general, TLPs are involved in host defense and a wide range of developmental processes in fungi, plants, and animals. TLG1 TLP is involved in lentinan degradation and fruiting body senescence. TLG1 expressed in Escherichia coli and Aspergillus oryzae exhibited beta-1,3-glucanase activity and demonstrated lentinan degrading activity. TLG1 is proposed to be involved in lentinan and cell wall degradation during senescence following harvest and spore diffusion. TLPs are three-domain, crescent-fold structures with either an electronegative, electropositive, or neutral cleft occurring between domains I and II. TLG1 from Lentinula edodes contains the required acidic amino acids conserved in the appropriate positions to possess an electronegative cleft. TLPs within this subfamily contain 13 conserve
Probab=21.89 E-value=2.5e+02 Score=18.53 Aligned_cols=21 Identities=14% Similarity=0.275 Sum_probs=16.1
Q ss_pred cccCCCCEEEEEEc-CC-CeeeE
Q psy88 50 CPITQGNTFRYQFT-AN-AGTHF 70 (75)
Q Consensus 50 ~~i~pG~~~~y~~~-~~-~Gt~~ 70 (75)
..+.||+++++..+ .- +|..|
T Consensus 32 f~L~pg~s~~i~vp~~w~~GRiW 54 (229)
T cd09219 32 WEAAAGGQVEFTVPDNWTAGRIW 54 (229)
T ss_pred EecCCCCeEEEECCCCCccccee
Confidence 34889999999998 43 37766
No 309
>TIGR02756 TraK_Ftype type-F conjugative transfer system secretin TraK. The TraK protein is predicted to interact with the TraV and TraB proteins as part of the scaffold which extends from the inner membrane, through the periplasm to the cell envelope and through which the F-type conjugative pilus passes. TraK is homologous to the P-type IV secretion system protein TrbG, the Ti-type protein VirB9 and the I-type TraN protein. The protein is related to the secretin family especially the HrcC subgroup of the type III secretion system. The protein is hypothesized to oligomerize to form a ring structure akin to other secretins.
Probab=21.85 E-value=1.1e+02 Score=19.92 Aligned_cols=21 Identities=5% Similarity=0.215 Sum_probs=18.2
Q ss_pred cccEEEecCCEEEEEEEeCCC
Q psy88 2 LYPKNVCEGDRVVVDVRNSMD 22 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~ 22 (75)
.++|.+..||++.+.+.|...
T Consensus 19 ~~~i~~~~~~~v~~~lS~~~~ 39 (232)
T TIGR02756 19 AVTVTFANGEDIAIALSSTDP 39 (232)
T ss_pred ceEEEccCCCeEEEEEecCCC
Confidence 468899999999999998754
No 310
>cd09218 TLP-PA allergenic/antifungal thaumatin-like proteins: plant and animal homologs. This subfamily is represented by the thaumatin-like proteins (TLPs), Cherry Allergen Pru Av 2 TLP, Peach PpAZ44 TLP (a propylene-induced TLP in abscission), the Caenorhabditis elegans thaumatin family member (thn-6), and other plant and animal homologs. TLPs are involved in host defense and a wide range of developmental processes in fungi, plants, and animals. Due to their inducible expression by environmental stresses such as pathogen/pest attack, drought and cold, plant TLPs are classified as the pathogenesis-related (PR) protein family 5 (PR5). Several members of the plant TLP family have been reported as food allergens from fruits (i.e., cherry, Pru av 2; bell pepper, Cap a1; tomatoes, Lyc e NP24) and pollen allergens from conifers (i.e., mountain cedar, Jun a 3; Arizona cypress, Cup a3; Japanese cedar, Cry j3). TLPs are three-domain, crescent-fold structures with either an electronegative, ele
Probab=21.83 E-value=2.4e+02 Score=18.39 Aligned_cols=22 Identities=9% Similarity=0.141 Sum_probs=17.1
Q ss_pred cccCCCCEEEEEEc-CCCeeeEE
Q psy88 50 CPITQGNTFRYQFT-ANAGTHFW 71 (75)
Q Consensus 50 ~~i~pG~~~~y~~~-~~~Gt~~Y 71 (75)
..+.||+++++..+ .-.|.+|=
T Consensus 30 f~L~~g~s~~~~vp~~WsGriWa 52 (219)
T cd09218 30 FELAPGQSRTIDAPSGWSGRFWG 52 (219)
T ss_pred EEcCCCCeEEEeCCCCcceeeee
Confidence 45889999999988 65677763
No 311
>cd05894 Ig_C5_MyBP-C C5 immunoglobulin (Ig) domain of cardiac myosin binding protein C (MyBP-C). Ig_C5_MyBP_C : the C5 immunoglobulin (Ig) domain of cardiac myosin binding protein C (MyBP-C). MyBP_C consists of repeated domains, Ig and fibronectin type 3, and various linkers. Three isoforms of MYBP_C exist and are included in this group: cardiac(c), and fast and slow skeletal muscle (s) MyBP_C. cMYBP_C has insertions between and inside domains and an additional cardiac-specific Ig domain at the N-terminus. For cMYBP_C an interaction has been demonstrated between this C5 domain and the Ig C8 domain.
Probab=21.83 E-value=1.4e+02 Score=15.71 Aligned_cols=27 Identities=26% Similarity=0.409 Sum_probs=19.8
Q ss_pred ccEEEecCCEEEEEEEeCCCCCCceEEe
Q psy88 3 YPKNVCEGDRVVVDVRNSMDGLENTIHW 30 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N~~~~~~~~iH~ 30 (75)
.++.+.+|+.+.+...=... .+-.+.|
T Consensus 3 ~~~~v~~G~~v~l~c~~~G~-P~P~v~W 29 (86)
T cd05894 3 NTIVVVAGNKLRLDVPISGE-PAPTVTW 29 (86)
T ss_pred CEEEEEcCCEEEEEeeEeec-CCCeEEE
Confidence 46889999999998875544 3446666
No 312
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=21.83 E-value=59 Score=18.58 Aligned_cols=15 Identities=27% Similarity=0.401 Sum_probs=10.6
Q ss_pred EEEecCCEEEEEEEe
Q psy88 5 KNVCEGDRVVVDVRN 19 (75)
Q Consensus 5 i~~~~Gd~v~i~~~N 19 (75)
+.++.||+|.|---+
T Consensus 3 ~~i~kGD~V~Vi~G~ 17 (105)
T PRK00004 3 MKIKKGDTVIVIAGK 17 (105)
T ss_pred CcccCCCEEEEeEcC
Confidence 467888988876443
No 313
>smart00042 CUB Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. This domain is found mostly among developmentally-regulated proteins. Spermadhesins contain only this domain.
Probab=21.79 E-value=86 Score=16.51 Aligned_cols=16 Identities=13% Similarity=0.196 Sum_probs=13.1
Q ss_pred cEEEecCCEEEEEEEe
Q psy88 4 PKNVCEGDRVVVDVRN 19 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N 19 (75)
.|++..|.+|+|++.-
T Consensus 21 ~i~~~~g~~i~l~f~~ 36 (102)
T smart00042 21 TIRAPPGYRIELQFTD 36 (102)
T ss_pred EEECCCCeEEEEEEEE
Confidence 5788889999998873
No 314
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=21.74 E-value=1e+02 Score=15.36 Aligned_cols=15 Identities=27% Similarity=0.142 Sum_probs=12.0
Q ss_pred EecCCEEEEEEEeCC
Q psy88 7 VCEGDRVVVDVRNSM 21 (75)
Q Consensus 7 ~~~Gd~v~i~~~N~~ 21 (75)
++.||.+++.+..-.
T Consensus 45 ~~~G~~i~v~v~~~d 59 (70)
T cd05698 45 FRVGQVVKVKVLSCD 59 (70)
T ss_pred ccCCCEEEEEEEEEc
Confidence 678999999987643
No 315
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=21.71 E-value=59 Score=16.44 Aligned_cols=12 Identities=33% Similarity=0.415 Sum_probs=8.8
Q ss_pred EEEecCCEEEEE
Q psy88 5 KNVCEGDRVVVD 16 (75)
Q Consensus 5 i~~~~Gd~v~i~ 16 (75)
..++.||+|+|-
T Consensus 48 ~~L~dgD~Ieiv 59 (65)
T PRK06488 48 FVLHEGDRIEIL 59 (65)
T ss_pred cccCCCCEEEEE
Confidence 457889988873
No 316
>cd09215 Thaumatin-like the sweet-tasting protein, thaumatin, and thaumatin-like proteins involved in host defense. This family is represented by the sweet-tasting protein thaumatin from the African berry Thaumatococcus daniellii and thaumatin-like proteins (TLPs) involved in host defense and a wide range of developmental processes in fungi, plants, and animals. Plant TLPs are classified as pathogenesis-related (PR) protein family 5 (PR5), their expression is induced by environmental stresses such as pathogen/pest attack, drought and cold. TLPs included in this family are such proteins as zeamatin, found in high concentrations in cereal seeds; osmotin, a salt-induced protein in osmotically stressed plants; and PpAZ44, a propylene-induced TLP in abscission of young fruit. Several members of the plant TLP family have been reported as food allergens from fruits (i.e., cherry, Pru av 2; bell pepper, Cap a1; tomatoes, Lyc e NP24) and pollen allergens from conifers (i.e., mountain cedar, Jun
Probab=21.70 E-value=2.1e+02 Score=17.65 Aligned_cols=21 Identities=14% Similarity=0.325 Sum_probs=16.4
Q ss_pred cccCCCCEEEEEEc-CCCeeeE
Q psy88 50 CPITQGNTFRYQFT-ANAGTHF 70 (75)
Q Consensus 50 ~~i~pG~~~~y~~~-~~~Gt~~ 70 (75)
..+.||+++++..+ .-.|..|
T Consensus 28 f~L~~g~s~~~~~p~~wsGriW 49 (157)
T cd09215 28 FELNPGETKSFDVSAGWQGRIW 49 (157)
T ss_pred EecCCCCeeEEecCCCCeEeee
Confidence 34889999999988 6567666
No 317
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=21.58 E-value=1.3e+02 Score=15.13 Aligned_cols=17 Identities=29% Similarity=0.172 Sum_probs=11.0
Q ss_pred EEecCCEEEEEEEeCCC
Q psy88 6 NVCEGDRVVVDVRNSMD 22 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~~~ 22 (75)
.++.||.|.+-+.....
T Consensus 37 ~~~~Gd~v~VFvY~D~~ 53 (61)
T PF13509_consen 37 PLKVGDEVEVFVYLDKE 53 (61)
T ss_dssp ---TTSEEEEEEEE-TT
T ss_pred CCCCCCEEEEEEEECCC
Confidence 57889999999887654
No 318
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=21.40 E-value=50 Score=18.05 Aligned_cols=15 Identities=7% Similarity=0.222 Sum_probs=8.9
Q ss_pred EEecCCEEEEEEEeC
Q psy88 6 NVCEGDRVVVDVRNS 20 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~ 20 (75)
+++.||+|.+.+...
T Consensus 42 ~L~pGq~l~f~~d~~ 56 (85)
T PF04225_consen 42 RLKPGQTLEFQLDED 56 (85)
T ss_dssp G--TT-EEEEEE-TT
T ss_pred hCCCCCEEEEEECCC
Confidence 578999999988654
No 319
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=21.22 E-value=77 Score=15.80 Aligned_cols=13 Identities=31% Similarity=0.672 Sum_probs=9.5
Q ss_pred EecCCEEEEEEEe
Q psy88 7 VCEGDRVVVDVRN 19 (75)
Q Consensus 7 ~~~Gd~v~i~~~N 19 (75)
+..||+|.+.+..
T Consensus 32 A~~gD~V~v~i~~ 44 (58)
T PF08206_consen 32 AMDGDKVLVRITP 44 (58)
T ss_dssp S-TT-EEEEEEEE
T ss_pred CCCCCEEEEEEec
Confidence 4569999999988
No 320
>PRK13782 phosphocarrier protein Chr; Provisional
Probab=21.20 E-value=50 Score=17.74 Aligned_cols=17 Identities=6% Similarity=0.147 Sum_probs=13.0
Q ss_pred ccEEEecCCEEEEEEEe
Q psy88 3 YPKNVCEGDRVVVDVRN 19 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N 19 (75)
+.|-+++||.|+|...-
T Consensus 51 lsLg~~~g~~v~v~~~G 67 (82)
T PRK13782 51 MSLAIGTGSMITIITEG 67 (82)
T ss_pred HhcCCCCCCEEEEEEeC
Confidence 45678889999988654
No 321
>TIGR03630 arch_S17P archaeal ribosomal protein S17P. This model describes exclusively the archaeal ribosomal protein S17P. It excludes homologous ribosomal proteins S11 from eukaryotes and S17 from bacteria.
Probab=21.09 E-value=56 Score=18.84 Aligned_cols=13 Identities=38% Similarity=0.539 Sum_probs=10.2
Q ss_pred EEEecCCEEEEEE
Q psy88 5 KNVCEGDRVVVDV 17 (75)
Q Consensus 5 i~~~~Gd~v~i~~ 17 (75)
..++.||+|+|.=
T Consensus 74 n~~kvGD~V~I~E 86 (102)
T TIGR03630 74 IDVKEGDIVIIGE 86 (102)
T ss_pred CCCCCCCEEEEEE
Confidence 3578999999863
No 322
>PF02933 CDC48_2: Cell division protein 48 (CDC48), domain 2; InterPro: IPR004201 This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the C terminus. The VAT-N domain found in AAA ATPases (IPR003959 from INTERPRO) is a substrate 185-residue recognition domain [].; GO: 0005524 ATP binding; PDB: 1QDN_B 1QCS_A 1CR5_C 3QQ8_A 3HU2_A 3HU1_E 3HU3_A 3QWZ_A 3TIW_B 3QQ7_A ....
Probab=21.09 E-value=1.1e+02 Score=15.44 Aligned_cols=14 Identities=29% Similarity=0.472 Sum_probs=9.5
Q ss_pred EEEecCCEEEEEEE
Q psy88 5 KNVCEGDRVVVDVR 18 (75)
Q Consensus 5 i~~~~Gd~v~i~~~ 18 (75)
.-+.+||.|.+.+.
T Consensus 17 ~pv~~Gd~i~~~~~ 30 (64)
T PF02933_consen 17 RPVTKGDTIVFPFF 30 (64)
T ss_dssp EEEETT-EEEEEET
T ss_pred CCccCCCEEEEEeC
Confidence 34678888888775
No 323
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=20.99 E-value=1.3e+02 Score=15.48 Aligned_cols=15 Identities=33% Similarity=0.328 Sum_probs=11.7
Q ss_pred EEecCCEEEEEEEeC
Q psy88 6 NVCEGDRVVVDVRNS 20 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~ 20 (75)
..+.||.|++.+...
T Consensus 48 ~~~~Gd~v~v~v~~v 62 (79)
T cd05684 48 VVKRGQKVKVKVISI 62 (79)
T ss_pred eeCCCCEEEEEEEEE
Confidence 358899999987764
No 324
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=20.95 E-value=55 Score=19.07 Aligned_cols=13 Identities=23% Similarity=0.312 Sum_probs=10.3
Q ss_pred EEEecCCEEEEEE
Q psy88 5 KNVCEGDRVVVDV 17 (75)
Q Consensus 5 i~~~~Gd~v~i~~ 17 (75)
..++.||.|+|.=
T Consensus 76 n~~kvGD~V~I~E 88 (108)
T PRK08572 76 IDAKVGDKVKIAE 88 (108)
T ss_pred CCCCCCCEEEEEE
Confidence 4588999999863
No 325
>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=20.85 E-value=1.1e+02 Score=18.33 Aligned_cols=14 Identities=29% Similarity=0.544 Sum_probs=13.2
Q ss_pred cccccCCCCEEEEE
Q psy88 48 TQCPITQGNTFRYQ 61 (75)
Q Consensus 48 ~~~~i~pG~~~~y~ 61 (75)
+.||+..|++.+|.
T Consensus 81 s~CP~~kGet~~Y~ 94 (130)
T cd00915 81 SFCGALKGETVYYV 94 (130)
T ss_pred ccCCccCCceEEEe
Confidence 68999999999999
No 326
>PF14801 GCD14_N: tRNA methyltransferase complex GCD14 subunit N-term; PDB: 1I9G_A.
Probab=20.80 E-value=78 Score=16.18 Aligned_cols=10 Identities=40% Similarity=0.587 Sum_probs=5.0
Q ss_pred EecCCEEEEE
Q psy88 7 VCEGDRVVVD 16 (75)
Q Consensus 7 ~~~Gd~v~i~ 16 (75)
++.||+|.++
T Consensus 6 f~~GdrVQlT 15 (54)
T PF14801_consen 6 FRAGDRVQLT 15 (54)
T ss_dssp --TT-EEEEE
T ss_pred CCCCCEEEEc
Confidence 4678887765
No 327
>cd00041 CUB CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
Probab=20.76 E-value=1.1e+02 Score=16.16 Aligned_cols=17 Identities=12% Similarity=0.133 Sum_probs=14.1
Q ss_pred cEEEecCCEEEEEEEeC
Q psy88 4 PKNVCEGDRVVVDVRNS 20 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N~ 20 (75)
.|++..|..|+|.|..-
T Consensus 31 ~i~~~~g~~i~l~f~~~ 47 (113)
T cd00041 31 TIEAPPGYRIRLTFEDF 47 (113)
T ss_pred EEEcCCCCEEEEEEeCc
Confidence 58889999999999853
No 328
>cd00305 Cu-Zn_Superoxide_Dismutase Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene causes familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Cytoplasmic and periplasmic SODs exist as dimers, whereas chloroplastic and extracellular enzymes exist as tetramers. Structure supports independent functional evolution in prokaryotes (P-class) and eukaryotes (E-class) [PMID:.8176730].
Probab=20.59 E-value=2e+02 Score=17.04 Aligned_cols=24 Identities=13% Similarity=0.106 Sum_probs=15.4
Q ss_pred CCEEEEEEEeCCCCCCceEEeCCcc
Q psy88 10 GDRVVVDVRNSMDGLENTIHWHGIH 34 (75)
Q Consensus 10 Gd~v~i~~~N~~~~~~~~iH~HG~~ 34 (75)
+-.|.+++.+-.+ -.+.+|.|-.-
T Consensus 26 ~v~v~~~l~GL~p-G~hg~HIHe~G 49 (144)
T cd00305 26 GVTITGELSGLTP-GLHGFHIHEFG 49 (144)
T ss_pred CEEEEEEEECCCC-CceeEEEEecC
Confidence 4556666666554 57788887643
No 329
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=20.57 E-value=1e+02 Score=15.82 Aligned_cols=15 Identities=13% Similarity=0.007 Sum_probs=12.2
Q ss_pred EecCCEEEEEEEeCC
Q psy88 7 VCEGDRVVVDVRNSM 21 (75)
Q Consensus 7 ~~~Gd~v~i~~~N~~ 21 (75)
++.||.|++.+.+..
T Consensus 49 ~~~Gd~v~~kV~~~~ 63 (72)
T cd05704 49 FKPGKIVRCCILSKK 63 (72)
T ss_pred CCCCCEEEEEEEEec
Confidence 477999999988764
No 330
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=20.51 E-value=1.1e+02 Score=15.50 Aligned_cols=17 Identities=18% Similarity=0.128 Sum_probs=13.1
Q ss_pred EEecCCEEEEEEEeCCC
Q psy88 6 NVCEGDRVVVDVRNSMD 22 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~~~ 22 (75)
+++.||.+.+.+.+-.+
T Consensus 42 ~~~~G~~i~~kVi~id~ 58 (66)
T cd05695 42 TYKEGQKVRARILYVDP 58 (66)
T ss_pred CcCCCCEEEEEEEEEeC
Confidence 37889999998886543
No 331
>PF04693 DDE_Tnp_2: Archaeal putative transposase ISC1217; InterPro: IPR006783 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the putative transposase ISC1217 from archaebacteria. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=20.49 E-value=48 Score=22.97 Aligned_cols=12 Identities=25% Similarity=0.299 Sum_probs=9.8
Q ss_pred CCCeeeEEccCC
Q psy88 64 ANAGTHFWHAHT 75 (75)
Q Consensus 64 ~~~Gt~~YH~H~ 75 (75)
..-|++||||++
T Consensus 105 s~~g~~~~~c~~ 116 (327)
T PF04693_consen 105 SRNGTYAFYCRT 116 (327)
T ss_pred ccCCcEEEEecc
Confidence 467999999974
No 332
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=20.41 E-value=99 Score=16.14 Aligned_cols=16 Identities=25% Similarity=0.304 Sum_probs=13.5
Q ss_pred EecCCEEEEEEEeCCC
Q psy88 7 VCEGDRVVVDVRNSMD 22 (75)
Q Consensus 7 ~~~Gd~v~i~~~N~~~ 22 (75)
++.||.+...+.+...
T Consensus 51 ~~~GD~i~~~V~~~~~ 66 (82)
T cd04454 51 LQPGDLILAKVISLGD 66 (82)
T ss_pred CCCCCEEEEEEEEeCC
Confidence 6899999999998654
No 333
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=20.40 E-value=85 Score=19.21 Aligned_cols=16 Identities=25% Similarity=0.198 Sum_probs=11.5
Q ss_pred cEEEecCCEEEEEEEe
Q psy88 4 PKNVCEGDRVVVDVRN 19 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~N 19 (75)
.+.++.||+|.|.--.
T Consensus 44 s~~IkkGD~V~Vi~Gk 59 (143)
T PTZ00194 44 SMPVRKDDEVMVVRGH 59 (143)
T ss_pred cceeecCCEEEEecCC
Confidence 3578899999886443
No 334
>cd08548 Type_I_cohesin_like Type I cohesin domain, interaction partner of dockerin. Bacterial cohesin domains bind to a complementary protein domain named dockerin, and this interaction is required for the formation of the cellulosome, a cellulose-degrading complex. The cellulosome consists of scaffoldin, a noncatalytic scaffolding polypeptide, that comprises repeating cohesion modules and a single carbohydrate-binding module (CBM). Specific calcium-dependent interactions between cohesins and dockerins appear to be essential for cellulosome assembly. This subfamily represents type I cohesins; their interactions with dockerin mediate assembly of a range of dockerin-borne enzymes to the complex.
Probab=20.34 E-value=1.3e+02 Score=17.67 Aligned_cols=15 Identities=33% Similarity=0.299 Sum_probs=11.5
Q ss_pred cEEEecCCEEEEEEE
Q psy88 4 PKNVCEGDRVVVDVR 18 (75)
Q Consensus 4 ~i~~~~Gd~v~i~~~ 18 (75)
...++.||+|.|-+.
T Consensus 7 ~v~~~~G~tv~VpV~ 21 (135)
T cd08548 7 SVSGKPGDTVTVPVT 21 (135)
T ss_pred cEEecCCCEEEEEEE
Confidence 357889999887765
No 335
>PF00963 Cohesin: Cohesin domain; InterPro: IPR002102 Cohesin domains interact with a complementary domain, termed the dockerin domain (see IPR002105 from INTERPRO). The cohesin-dockerin interaction is the crucial interaction for complex formation in the cellulosome []. The scaffoldin component of the cellulolytic bacterium Clostridium thermocellum is a non-hydrolytic protein which organises the hydrolytic enzymes in a large complex, called the cellulosome. Scaffoldin comprises a series of functional domains, amongst which is a single cellulose-binding domain and nine cohesin domains which are responsible for integrating the individual enzymatic subunits into the complex.; GO: 0030246 carbohydrate binding, 0000272 polysaccharide catabolic process; PDB: 2BM3_A 3P0D_I 3KCP_A 2B59_A 3L8Q_B 3FNK_C 3GHP_B 2CCL_A 1ANU_A 1OHZ_A ....
Probab=20.30 E-value=1.2e+02 Score=17.50 Aligned_cols=14 Identities=29% Similarity=0.356 Sum_probs=10.8
Q ss_pred EEEecCCEEEEEEE
Q psy88 5 KNVCEGDRVVVDVR 18 (75)
Q Consensus 5 i~~~~Gd~v~i~~~ 18 (75)
..++.||+|.|.+.
T Consensus 8 ~~a~~G~tv~V~V~ 21 (141)
T PF00963_consen 8 VSAKPGETVTVPVN 21 (141)
T ss_dssp CEE-TTSEEEEEEE
T ss_pred ceECCCCEEEEEEE
Confidence 46789999998887
No 336
>cd07690 Ig1_CD4 First immunoglobulin (Ig) domain of CD4. Ig1_CD4; first immunoglobulin (Ig) domain of CD4. CD4 and CD8 are the two primary co-receptor proteins found on the surface of T cells, and the presence of either CD4 or CD8 determines the function of the T cell. CD4 is found on helper T cells, where it is required for the binding of MHC (major histocompatibility complex) class II molecules, while CD8 is found on cytotoxic T cells, where it is required for the binding of MHC class I molecules. CD4 contains four immunoglobulin domains, with the first three included in this hierarchy. The fourth domain has a general Ig architecture, but has slight topological changes in the arrangement of beta strands relative to the other structures in this family and is not specifically included in the hierarchy.
Probab=20.25 E-value=1.7e+02 Score=16.05 Aligned_cols=26 Identities=19% Similarity=0.247 Sum_probs=19.5
Q ss_pred EEEecCCEEEEEEEeCCCCCCceEEeC
Q psy88 5 KNVCEGDRVVVDVRNSMDGLENTIHWH 31 (75)
Q Consensus 5 i~~~~Gd~v~i~~~N~~~~~~~~iH~H 31 (75)
+.+++||+|.+.=.=... ....|+|.
T Consensus 2 v~~~~G~~VtL~C~~s~~-~~~~i~W~ 27 (94)
T cd07690 2 VLGKKGDTAELPCTASQK-KSIQFHWK 27 (94)
T ss_pred eEeeCCCCEEEEEEeCCC-CCcEEEEE
Confidence 578999999998765433 45678885
No 337
>COG1278 CspC Cold shock proteins [Transcription]
Probab=20.18 E-value=95 Score=16.50 Aligned_cols=17 Identities=24% Similarity=0.431 Sum_probs=13.6
Q ss_pred EEecCCEEEEEEEeCCC
Q psy88 6 NVCEGDRVVVDVRNSMD 22 (75)
Q Consensus 6 ~~~~Gd~v~i~~~N~~~ 22 (75)
++++||+|.+.+.+...
T Consensus 41 ~L~eGQ~V~f~~~~g~k 57 (67)
T COG1278 41 TLREGQKVEFEVEQGRK 57 (67)
T ss_pred ccCCCCEEEEEEecCCC
Confidence 46789999999888653
No 338
>cd05717 Ig1_Necl-1-3_like First (N-terminal) immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 - Necl-3 (also known as cell adhesion molecules CADM3, CADM1, and CADM2 respectively). Ig1_Necl-1-3_like: N-terminal immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 (also known as cell adhesion molecule 3 (CADM3)), Necl-2 (CADM1), and Necl-3 (CADM2). At least five nectin-like molecules have been identified (Necl-1 - Necl-5). They all have an extracellular region containing three Ig-like domains, a transmembrane region, and a cytoplasmic region. The N-terminal Ig-like domain of the extracellular region belongs to the V-type subfamily of Ig domains, is essential to cell-cell adhesion, and plays a part in the interaction with the envelope glycoprotein D of various viruses. Necl-1, Necl-2, and Necl-3 have Ca(2+)-independent homophilic and heterophilic cell-cell adhesion activity. Necl-1 is specifically expressed in neural tissue, and is important to the form
Probab=20.14 E-value=1.6e+02 Score=15.56 Aligned_cols=28 Identities=18% Similarity=0.385 Sum_probs=19.6
Q ss_pred ccEEEecCCEEEEEEEeCCCCCCceEEeC
Q psy88 3 YPKNVCEGDRVVVDVRNSMDGLENTIHWH 31 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N~~~~~~~~iH~H 31 (75)
..+.+.+|+.+.++=.=... ....+.|-
T Consensus 5 ~~~~v~~G~~v~L~C~~~~~-~~~~v~W~ 32 (95)
T cd05717 5 QDVTVVEGGTATLKCRVKNN-DNSSLQWS 32 (95)
T ss_pred CcEEEcCCCCEEEEEEECCC-CCceEEEe
Confidence 46789999999997654333 24578883
No 339
>PRK13780 phosphocarrier protein HPr; Provisional
Probab=20.04 E-value=56 Score=17.96 Aligned_cols=18 Identities=11% Similarity=0.303 Sum_probs=13.8
Q ss_pred ccEEEecCCEEEEEEEeC
Q psy88 3 YPKNVCEGDRVVVDVRNS 20 (75)
Q Consensus 3 ~~i~~~~Gd~v~i~~~N~ 20 (75)
+.|-++.||.|+|...-.
T Consensus 51 m~Lg~~~G~~v~i~a~G~ 68 (88)
T PRK13780 51 MSLGVGQGADITISAEGA 68 (88)
T ss_pred HhcCCCCCCEEEEEEeCc
Confidence 456788999999987643
No 340
>cd05749 Ig2_Tyro3_like Second immunoglobulin (Ig)-like domain of Axl/Tyro3 receptor tyrosine kinases (RTKs). Ig2_Tyro3_like: the second immunoglobulin (Ig)-like domain in the Axl/Tyro3 family of receptor tyrosine kinases (RTKs). This family includes Axl (also known as Ark, Ufo, and Tyro7), Tyro3 (also known as Sky, Rse, Brt, Dtk, and Tif), and Mer (also known as Nyk, c-Eyk, and Tyro12). Axl/Tyro3 family receptors have an extracellular portion with two Ig-like domains followed by two fibronectin-types III (FNIII) domains, a membrane-spanning single helix, and a cytoplasmic tyrosine kinase domain. Axl, Tyro3 and Mer are widely expressed in adult tissues, though they show higher expression in the brain, in the lymphatic and vascular systems, and in the testis. Axl, Tyro3, and Mer bind the vitamin K dependent protein Gas6 with high affinity, and in doing so activate their tyrosine kinase activity. Axl/Gas6 signaling may play a part in cell adhesion processes, prevention of apoptosis, and c
Probab=20.02 E-value=1.6e+02 Score=15.55 Aligned_cols=29 Identities=10% Similarity=0.006 Sum_probs=20.0
Q ss_pred cccEEEecCCEEEEEEEeCCCCCCceEEe
Q psy88 2 LYPKNVCEGDRVVVDVRNSMDGLENTIHW 30 (75)
Q Consensus 2 ~~~i~~~~Gd~v~i~~~N~~~~~~~~iH~ 30 (75)
+..+.+.+|+.+.+.-.=.....|..|.|
T Consensus 5 P~~~~v~~G~~v~l~C~a~G~P~P~~I~W 33 (81)
T cd05749 5 PEDLSVTANTPFNLTCQAVGPPEPVEILW 33 (81)
T ss_pred CCceEEcCCCCEEEEEEeeeecCCeEEEE
Confidence 34578899999999887544313445777
Done!