Query 022290
Match_columns 299
No_of_seqs 331 out of 1170
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 02:23:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022290.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022290hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08325 WLM: WLM domain; Int 100.0 8.2E-43 1.8E-47 310.0 14.2 150 1-166 33-186 (186)
2 KOG4842 Protein involved in si 99.8 7.3E-19 1.6E-23 161.6 6.7 163 1-178 62-237 (278)
3 PF01863 DUF45: Protein of unk 99.6 1.7E-15 3.6E-20 134.2 5.2 64 18-87 137-200 (205)
4 COG1451 Predicted metal-depend 99.3 2E-12 4.4E-17 118.3 4.5 64 18-87 148-211 (223)
5 KOG4842 Protein involved in si 99.2 9.2E-12 2E-16 115.0 4.3 87 1-89 149-241 (278)
6 PF00641 zf-RanBP: Zn-finger i 98.4 1.6E-07 3.4E-12 60.0 1.5 27 225-251 3-29 (30)
7 PF00641 zf-RanBP: Zn-finger i 98.3 2.2E-07 4.8E-12 59.3 1.2 29 257-285 2-30 (30)
8 smart00731 SprT SprT homologue 98.1 1.1E-06 2.3E-11 75.3 2.0 58 20-81 32-95 (146)
9 KOG4198 RNA-binding Ran Zn-fin 98.1 1.8E-06 4E-11 81.5 3.4 68 220-287 58-168 (280)
10 smart00547 ZnF_RBZ Zinc finger 97.7 1.5E-05 3.3E-10 48.9 1.4 24 226-249 2-25 (26)
11 smart00547 ZnF_RBZ Zinc finger 97.6 2.6E-05 5.6E-10 47.9 1.5 25 258-282 1-25 (26)
12 PF10263 SprT-like: SprT-like 97.3 0.00015 3.3E-09 61.7 3.3 60 17-80 27-97 (157)
13 PF12773 DZR: Double zinc ribb 97.1 0.00049 1.1E-08 48.3 3.3 50 229-280 1-50 (50)
14 KOG4198 RNA-binding Ran Zn-fin 97.1 0.00041 8.9E-09 65.8 3.5 32 221-252 135-166 (280)
15 KOG4477 RING1 interactor RYBP 96.1 0.0028 6.1E-08 56.8 1.9 34 220-253 18-51 (228)
16 PRK04351 hypothetical protein; 96.0 0.0071 1.5E-07 52.5 3.8 46 29-78 43-95 (149)
17 KOG4477 RING1 interactor RYBP 95.9 0.0022 4.7E-08 57.5 0.4 32 255-286 20-51 (228)
18 PRK14559 putative protein seri 95.9 0.0062 1.3E-07 64.0 3.7 50 228-284 3-52 (645)
19 COG3091 SprT Zn-dependent meta 95.4 0.013 2.9E-07 51.0 3.1 33 47-79 57-96 (156)
20 PRK04860 hypothetical protein; 94.9 0.018 3.8E-07 50.6 2.4 46 29-78 45-97 (160)
21 KOG4345 NF-kappa B regulator A 94.3 0.0048 1E-07 64.5 -2.8 60 224-283 5-115 (774)
22 KOG4345 NF-kappa B regulator A 92.7 0.056 1.2E-06 56.8 1.7 68 220-287 85-213 (774)
23 PF13485 Peptidase_MA_2: Pepti 92.0 0.12 2.6E-06 40.9 2.4 39 23-68 4-42 (128)
24 cd00350 rubredoxin_like Rubred 90.3 0.16 3.6E-06 32.9 1.4 26 259-284 1-28 (33)
25 PF06114 DUF955: Domain of unk 90.3 0.37 8E-06 37.7 3.7 58 21-86 18-77 (122)
26 PF13248 zf-ribbon_3: zinc-rib 89.6 0.21 4.5E-06 30.8 1.4 23 260-282 3-25 (26)
27 PF04450 BSP: Peptidase of pla 89.1 0.24 5.1E-06 45.2 2.0 57 30-87 74-132 (205)
28 COG4219 MecR1 Antirepressor re 88.3 0.27 5.8E-06 47.9 1.8 29 38-66 177-205 (337)
29 PF08325 WLM: WLM domain; Int 88.2 1.2 2.6E-05 40.0 5.9 79 49-128 84-185 (186)
30 PF05569 Peptidase_M56: BlaR1 87.8 0.84 1.8E-05 42.9 4.9 26 46-71 191-216 (299)
31 PF13248 zf-ribbon_3: zinc-rib 87.2 0.37 8E-06 29.7 1.4 24 226-249 2-25 (26)
32 KOG3931 Uncharacterized conser 87.1 1 2.2E-05 44.4 5.1 55 23-79 77-142 (484)
33 COG0501 HtpX Zn-dependent prot 87.0 0.63 1.4E-05 43.2 3.5 58 5-68 117-174 (302)
34 PF13240 zinc_ribbon_2: zinc-r 86.9 0.37 8.1E-06 29.0 1.3 21 262-282 2-22 (23)
35 cd04270 ZnMc_TACE_like Zinc-de 86.8 0.53 1.2E-05 43.6 2.9 27 45-71 161-187 (244)
36 cd00729 rubredoxin_SM Rubredox 86.5 0.38 8.2E-06 31.6 1.2 26 259-284 2-29 (34)
37 PRK02870 heat shock protein Ht 85.5 0.92 2E-05 44.4 3.9 44 18-66 145-188 (336)
38 PRK04897 heat shock protein Ht 85.5 0.53 1.1E-05 44.9 2.2 43 21-68 112-154 (298)
39 PRK03072 heat shock protein Ht 85.5 0.54 1.2E-05 44.7 2.2 24 45-68 121-144 (288)
40 PF12388 Peptidase_M57: Dual-a 84.3 1.1 2.5E-05 41.1 3.7 41 25-71 113-153 (211)
41 PRK03982 heat shock protein Ht 84.2 0.65 1.4E-05 43.9 2.1 44 21-69 100-143 (288)
42 PRK14714 DNA polymerase II lar 83.5 1.1 2.5E-05 50.3 3.9 54 226-287 667-723 (1337)
43 PF01435 Peptidase_M48: Peptid 83.2 0.6 1.3E-05 41.2 1.4 38 29-70 71-108 (226)
44 PRK05457 heat shock protein Ht 83.1 0.77 1.7E-05 43.6 2.1 21 46-66 129-149 (284)
45 PRK03001 M48 family peptidase; 83.0 0.81 1.8E-05 43.2 2.3 41 21-66 99-139 (283)
46 PRK02391 heat shock protein Ht 82.6 0.82 1.8E-05 43.7 2.1 22 45-66 127-148 (296)
47 PRK01345 heat shock protein Ht 82.5 0.82 1.8E-05 44.1 2.1 41 21-66 99-139 (317)
48 PRK01265 heat shock protein Ht 81.3 0.96 2.1E-05 44.0 2.1 42 21-67 115-156 (324)
49 PF13240 zinc_ribbon_2: zinc-r 80.6 0.98 2.1E-05 27.2 1.2 22 228-249 1-22 (23)
50 KOG3854 SPRT-like metalloprote 80.6 1.1 2.4E-05 45.5 2.4 42 29-76 335-383 (505)
51 cd00730 rubredoxin Rubredoxin; 80.1 1.1 2.3E-05 32.1 1.5 9 258-266 33-41 (50)
52 COG5100 NPL4 Nuclear pore prot 79.6 0.47 1E-05 47.5 -0.6 25 259-283 546-570 (571)
53 cd04271 ZnMc_ADAM_fungal Zinc- 78.7 0.8 1.7E-05 42.1 0.6 18 53-70 147-164 (228)
54 COG1592 Rubrerythrin [Energy p 78.2 1.1 2.4E-05 39.7 1.3 10 226-235 134-143 (166)
55 PF01447 Peptidase_M4: Thermol 77.5 1.5 3.2E-05 38.1 1.9 21 43-63 127-147 (150)
56 KOG1995 Conserved Zn-finger pr 77.5 1.2 2.6E-05 43.7 1.4 61 223-285 68-149 (351)
57 PF10026 DUF2268: Predicted Zn 77.3 2.8 6E-05 37.5 3.6 47 30-81 49-98 (195)
58 COG4900 Predicted metallopepti 77.0 3.9 8.5E-05 34.4 4.1 47 26-76 59-113 (133)
59 COG5100 NPL4 Nuclear pore prot 76.0 0.65 1.4E-05 46.6 -0.8 25 226-250 546-570 (571)
60 PF13699 DUF4157: Domain of un 74.0 2.2 4.7E-05 33.1 1.8 32 29-65 44-75 (79)
61 cd04272 ZnMc_salivary_gland_MP 73.0 2 4.3E-05 38.8 1.6 19 52-70 146-164 (220)
62 PF13582 Reprolysin_3: Metallo 72.1 1.6 3.4E-05 35.2 0.7 16 53-68 109-124 (124)
63 cd04267 ZnMc_ADAM_like Zinc-de 71.3 2.1 4.6E-05 37.4 1.3 22 49-70 131-152 (192)
64 PF14521 Aspzincin_M35: Lysine 70.1 3.4 7.4E-05 35.5 2.3 23 49-71 94-116 (148)
65 PF13688 Reprolysin_5: Metallo 69.8 3.1 6.6E-05 36.4 2.0 25 46-70 137-161 (196)
66 cd04269 ZnMc_adamalysin_II_lik 69.8 3.5 7.6E-05 36.1 2.4 23 48-70 128-150 (194)
67 PF10058 DUF2296: Predicted in 69.0 2.6 5.7E-05 30.6 1.2 35 235-269 17-54 (54)
68 PF13574 Reprolysin_2: Metallo 68.2 2.3 5E-05 37.2 0.9 20 51-70 111-130 (173)
69 PF12773 DZR: Double zinc ribb 66.7 4.4 9.6E-05 28.0 1.9 25 223-247 26-50 (50)
70 PF09768 Peptidase_M76: Peptid 65.5 5 0.00011 35.8 2.5 19 45-63 65-83 (173)
71 PRK15410 DgsA anti-repressor M 65.4 5.9 0.00013 37.6 3.1 62 20-86 116-188 (260)
72 PF01421 Reprolysin: Reprolysi 65.0 4.8 0.00011 35.5 2.3 25 46-70 126-150 (199)
73 PF06262 DUF1025: Possibl zinc 64.5 4.4 9.5E-05 32.8 1.8 16 49-64 71-86 (97)
74 PF00301 Rubredoxin: Rubredoxi 64.4 2.7 5.8E-05 29.7 0.5 10 257-266 32-41 (47)
75 KOG1995 Conserved Zn-finger pr 64.3 6.3 0.00014 38.8 3.1 32 222-253 214-246 (351)
76 COG4260 Membrane protease subu 62.8 5 0.00011 38.8 2.0 52 33-91 125-177 (345)
77 KOG0957 PHD finger protein [Ge 62.1 11 0.00024 39.0 4.5 62 219-282 111-191 (707)
78 PF02102 Peptidase_M35: Deuter 61.8 4.3 9.3E-05 40.2 1.5 21 50-70 296-318 (359)
79 COG0308 PepN Aminopeptidase N 61.5 5.2 0.00011 43.7 2.2 22 46-67 302-323 (859)
80 PF00413 Peptidase_M10: Matrix 61.2 4.5 9.8E-05 33.6 1.3 24 46-69 100-123 (154)
81 cd04273 ZnMc_ADAMTS_like Zinc- 60.9 2.2 4.7E-05 38.2 -0.7 20 51-70 140-159 (207)
82 PF06167 Peptidase_M90: Glucos 60.9 8.1 0.00018 36.3 3.1 66 20-88 126-202 (253)
83 PF12725 DUF3810: Protein of u 58.3 3 6.5E-05 40.4 -0.3 46 46-91 191-238 (318)
84 cd04278 ZnMc_MMP Zinc-dependen 57.5 11 0.00024 31.9 3.2 40 30-69 86-125 (157)
85 PF13203 DUF2201_N: Putative m 57.4 7.6 0.00016 36.4 2.3 57 29-90 42-108 (292)
86 COG1773 Rubredoxin [Energy pro 57.3 5.6 0.00012 29.2 1.1 40 226-267 3-44 (55)
87 TIGR02414 pepN_proteo aminopep 56.4 6 0.00013 43.4 1.6 20 47-66 279-298 (863)
88 cd00203 ZnMc Zinc-dependent me 55.9 5.9 0.00013 33.3 1.2 22 49-70 94-115 (167)
89 PF15639 Tox-MPTase3: Metallop 55.8 4.8 0.0001 34.4 0.6 34 28-62 71-111 (135)
90 PRK14015 pepN aminopeptidase N 55.6 5.7 0.00012 43.6 1.3 19 48-66 293-311 (875)
91 cd04268 ZnMc_MMP_like Zinc-dep 54.9 8.9 0.00019 32.3 2.1 22 49-70 92-113 (165)
92 PF13058 DUF3920: Protein of u 54.6 5.4 0.00012 33.4 0.7 20 45-64 70-89 (126)
93 PRK04023 DNA polymerase II lar 54.6 14 0.0003 41.2 4.0 53 224-286 624-676 (1121)
94 COG4324 Predicted aminopeptida 54.4 21 0.00045 34.5 4.6 48 46-93 192-240 (376)
95 PF01433 Peptidase_M1: Peptida 53.8 10 0.00022 36.4 2.5 19 48-66 292-310 (390)
96 PF10023 DUF2265: Predicted am 53.5 22 0.00048 35.0 4.8 41 45-85 159-200 (337)
97 TIGR02412 pepN_strep_liv amino 52.5 8.1 0.00018 42.0 1.8 19 48-66 284-302 (831)
98 cd04277 ZnMc_serralysin_like Z 52.2 17 0.00036 31.8 3.5 38 30-69 94-131 (186)
99 PF03833 PolC_DP2: DNA polymer 52.2 4.7 0.0001 43.9 0.0 51 225-285 654-704 (900)
100 PF10460 Peptidase_M30: Peptid 51.6 7 0.00015 38.8 1.1 41 25-66 114-154 (366)
101 PRK04136 rpl40e 50S ribosomal 50.8 9.1 0.0002 27.3 1.3 25 225-249 13-37 (48)
102 PF04810 zf-Sec23_Sec24: Sec23 50.1 7.8 0.00017 26.1 0.8 13 258-270 23-35 (40)
103 TIGR02411 leuko_A4_hydro leuko 50.1 11 0.00023 39.7 2.2 16 51-66 279-294 (601)
104 cd04279 ZnMc_MMP_like_1 Zinc-d 50.0 12 0.00025 31.8 2.0 23 48-70 101-123 (156)
105 PRK11788 tetratricopeptide rep 47.0 12 0.00025 35.4 1.8 28 256-283 351-378 (389)
106 PRK14873 primosome assembly pr 45.8 14 0.0003 39.5 2.2 50 227-284 384-433 (665)
107 COG1592 Rubrerythrin [Energy p 45.4 12 0.00026 33.3 1.4 23 240-266 134-156 (166)
108 smart00235 ZnMc Zinc-dependent 44.9 10 0.00022 31.4 0.9 18 53-70 88-105 (140)
109 PRK04136 rpl40e 50S ribosomal 44.9 14 0.0003 26.4 1.4 24 258-281 13-36 (48)
110 KOG1046 Puromycin-sensitive am 44.8 13 0.00028 40.9 1.9 19 48-66 321-339 (882)
111 PF13583 Reprolysin_4: Metallo 44.8 12 0.00025 33.8 1.3 18 53-70 139-156 (206)
112 KOG1244 Predicted transcriptio 44.5 8.5 0.00018 37.0 0.4 41 226-266 275-329 (336)
113 PF10571 UPF0547: Uncharacteri 44.1 13 0.00029 23.0 1.1 22 261-282 2-23 (26)
114 PRK13130 H/ACA RNA-protein com 43.7 19 0.00041 26.4 2.1 29 259-289 5-33 (56)
115 KOG3658 Tumor necrosis factor- 42.2 15 0.00033 39.3 1.8 46 26-71 365-412 (764)
116 KOG3607 Meltrins, fertilins an 41.9 15 0.00032 39.7 1.7 22 48-69 320-341 (716)
117 PF10463 Peptidase_U49: Peptid 41.9 17 0.00038 33.3 2.0 19 51-69 101-119 (206)
118 PRK13267 archaemetzincin-like 41.8 20 0.00043 32.0 2.3 23 48-70 122-144 (179)
119 COG1198 PriA Primosomal protei 41.6 21 0.00046 38.6 2.8 49 227-282 436-484 (730)
120 PRK14714 DNA polymerase II lar 41.0 30 0.00066 39.6 4.0 50 240-298 667-716 (1337)
121 COG3058 FdhE Uncharacterized p 40.5 7.6 0.00016 37.4 -0.6 49 235-284 181-236 (308)
122 PRK05452 anaerobic nitric oxid 39.6 14 0.00031 37.6 1.2 29 257-285 423-470 (479)
123 PF01457 Peptidase_M8: Leishma 39.0 22 0.00048 36.6 2.5 32 31-66 194-225 (521)
124 TIGR00595 priA primosomal prot 39.0 24 0.00051 36.3 2.7 51 226-283 213-263 (505)
125 COG0675 Transposase and inacti 38.2 15 0.00032 33.9 1.0 27 241-273 310-336 (364)
126 PF07282 OrfB_Zn_ribbon: Putat 37.8 21 0.00046 26.1 1.6 29 241-270 29-57 (69)
127 COG2856 Predicted Zn peptidase 37.7 24 0.00051 32.5 2.2 22 47-68 68-89 (213)
128 PF14891 Peptidase_M91: Effect 37.4 11 0.00023 33.1 -0.1 19 52-70 104-122 (174)
129 PF15641 Tox-MPTase5: Metallop 37.2 48 0.001 26.8 3.6 39 42-80 55-105 (109)
130 PF12898 Stc1: Stc1 domain; I 36.5 32 0.00069 26.9 2.5 28 257-285 35-62 (84)
131 cd04327 ZnMc_MMP_like_3 Zinc-d 35.8 23 0.00051 31.4 1.8 19 50-68 91-109 (198)
132 PHA02456 zinc metallopeptidase 35.6 19 0.00041 30.4 1.1 15 50-64 78-92 (141)
133 PF07998 Peptidase_M54: Peptid 35.5 25 0.00055 31.9 2.0 50 19-70 111-164 (194)
134 PF05548 Peptidase_M11: Gameto 34.5 20 0.00044 34.7 1.3 43 20-70 127-169 (314)
135 PRK09672 phage exclusion prote 33.8 22 0.00048 34.5 1.4 17 50-66 164-180 (305)
136 TIGR00595 priA primosomal prot 33.5 29 0.00063 35.6 2.3 40 223-268 219-262 (505)
137 COG2093 DNA-directed RNA polym 33.4 22 0.00048 26.8 1.0 25 260-284 5-29 (64)
138 KOG3314 Ku70-binding protein [ 33.2 47 0.001 29.8 3.2 18 46-63 86-103 (194)
139 KOG2760 Vacuolar sorting prote 33.2 34 0.00074 34.5 2.6 47 222-268 86-139 (432)
140 COG1997 RPL43A Ribosomal prote 32.2 25 0.00053 28.2 1.2 29 241-270 36-64 (89)
141 COG5141 PHD zinc finger-contai 32.0 16 0.00035 37.8 0.2 54 227-281 194-255 (669)
142 COG3227 LasB Zinc metalloprote 30.2 13 0.00029 38.2 -0.8 38 23-63 308-349 (507)
143 COG1552 RPL40A Ribosomal prote 29.4 13 0.00027 26.8 -0.8 23 227-249 15-37 (50)
144 PF10103 DUF2342: Uncharacteri 29.2 33 0.00071 33.8 1.8 37 46-82 152-188 (342)
145 PF14445 Prok-RING_2: Prokaryo 28.9 5.4 0.00012 28.9 -2.7 41 226-280 7-48 (57)
146 PF02318 FYVE_2: FYVE-type zin 28.7 23 0.0005 29.1 0.5 42 228-282 56-103 (118)
147 COG3824 Predicted Zn-dependent 28.3 28 0.00061 29.7 1.0 15 49-63 107-121 (136)
148 PF13398 Peptidase_M50B: Pepti 27.7 34 0.00075 30.6 1.5 18 46-64 18-35 (200)
149 cd04283 ZnMc_hatching_enzyme Z 27.5 30 0.00065 31.0 1.1 16 52-67 78-93 (182)
150 PRK05580 primosome assembly pr 27.2 45 0.00097 35.6 2.5 41 241-283 391-431 (679)
151 cd04276 ZnMc_MMP_like_2 Zinc-d 27.2 44 0.00096 30.2 2.1 20 49-68 114-133 (197)
152 TIGR03624 putative hydrolase. 27.1 55 0.0012 32.3 2.9 37 46-82 151-187 (345)
153 TIGR03883 DUF2342_F420 unchara 27.1 58 0.0012 32.2 3.0 37 46-82 155-191 (346)
154 PRK03564 formate dehydrogenase 26.6 50 0.0011 32.1 2.5 29 56-87 41-69 (309)
155 KOG1047 Bifunctional leukotrie 26.6 32 0.00069 36.2 1.2 18 49-66 286-303 (613)
156 KOG0956 PHD finger protein AF1 26.4 31 0.00066 37.2 1.0 27 255-281 44-70 (900)
157 COG4783 Putative Zn-dependent 26.4 37 0.0008 35.0 1.6 35 29-66 111-145 (484)
158 cd04281 ZnMc_BMP1_TLD Zinc-dep 26.3 31 0.00067 31.3 1.0 17 52-68 88-104 (200)
159 PRK12286 rpmF 50S ribosomal pr 26.3 48 0.001 24.3 1.8 31 235-271 22-52 (57)
160 PRK14873 primosome assembly pr 26.2 45 0.00098 35.7 2.3 22 260-281 393-418 (665)
161 KOG0593 Predicted protein kina 26.1 51 0.0011 32.7 2.4 37 45-81 77-113 (396)
162 PF14247 DUF4344: Domain of un 25.8 46 0.00099 30.8 2.0 21 49-69 90-110 (220)
163 PF15640 Tox-MPTase4: Metallop 25.5 64 0.0014 27.6 2.6 49 1-63 31-81 (132)
164 PRK12496 hypothetical protein; 25.5 41 0.00088 29.5 1.5 10 154-163 81-90 (164)
165 PF14446 Prok-RING_1: Prokaryo 25.1 37 0.0008 24.8 1.0 40 241-283 6-51 (54)
166 TIGR01562 FdhE formate dehydro 24.4 53 0.0011 31.9 2.2 41 47-87 25-65 (305)
167 PRK11788 tetratricopeptide rep 24.4 44 0.00096 31.5 1.7 28 222-249 350-377 (389)
168 cd06158 S2P-M50_like_1 Unchara 24.3 47 0.001 29.4 1.7 14 50-63 8-21 (181)
169 PF02163 Peptidase_M50: Peptid 24.3 47 0.001 28.8 1.7 14 50-63 6-19 (192)
170 PF08271 TF_Zn_Ribbon: TFIIB z 24.2 29 0.00063 23.4 0.3 27 242-268 2-28 (43)
171 cd04282 ZnMc_meprin Zinc-depen 24.2 34 0.00074 31.8 0.8 17 52-68 121-137 (230)
172 PRK06393 rpoE DNA-directed RNA 23.1 49 0.0011 25.0 1.3 21 260-282 6-26 (64)
173 KOG2041 WD40 repeat protein [G 23.0 84 0.0018 34.4 3.5 60 225-284 1116-1185(1189)
174 PF08434 CLCA_N: Calcium-activ 22.8 19 0.00041 34.3 -1.2 38 25-65 124-163 (262)
175 KOG4443 Putative transcription 22.4 40 0.00088 36.0 1.0 17 225-249 61-77 (694)
176 cd04280 ZnMc_astacin_like Zinc 22.4 39 0.00085 29.7 0.8 17 52-68 75-91 (180)
177 cd06162 S2P-M50_PDZ_SREBP Ster 22.4 52 0.0011 31.5 1.7 14 50-63 134-147 (277)
178 PRK04023 DNA polymerase II lar 22.3 70 0.0015 36.0 2.8 47 231-285 617-663 (1121)
179 smart00661 RPOL9 RNA polymeras 21.9 72 0.0016 21.8 2.0 31 242-272 2-33 (52)
180 PF01400 Astacin: Astacin (Pep 21.8 39 0.00084 30.0 0.7 17 52-68 80-96 (191)
181 cd06258 Peptidase_M3_like The 21.7 70 0.0015 30.7 2.5 50 32-82 135-198 (365)
182 PF14319 Zn_Tnp_IS91: Transpos 21.5 69 0.0015 26.3 2.0 24 259-282 42-69 (111)
183 PRK08351 DNA-directed RNA poly 21.4 60 0.0013 24.3 1.5 21 261-283 5-25 (61)
184 KOG2719 Metalloprotease [Gener 20.9 50 0.0011 33.6 1.3 45 18-65 250-294 (428)
185 cd05709 S2P-M50 Site-2 proteas 20.8 60 0.0013 28.0 1.7 14 50-63 7-20 (180)
186 cd06164 S2P-M50_SpoIVFB_CBS Sp 20.7 60 0.0013 29.8 1.7 14 50-63 52-65 (227)
187 PF01432 Peptidase_M3: Peptida 20.3 84 0.0018 31.3 2.8 34 31-65 222-256 (458)
188 PRK05580 primosome assembly pr 20.1 72 0.0016 34.0 2.4 34 228-267 392-429 (679)
189 PF09538 FYDLN_acid: Protein o 20.0 99 0.0022 25.5 2.7 29 258-286 8-39 (108)
No 1
>PF08325 WLM: WLM domain; InterPro: IPR013536 The WLM (WSS1-like metalloprotease) domain is a globular domain related to the zincin-like superfamily of Zn-dependent peptidase. Since the WLM domain contains all known active site residues of zincins, it is predicted to be a catalytically active peptidase domain. The WLM domain is a eukaryotic domain represented in plants, fungi, Plasmodium, and kinetoplastids. By contrast, it is absent in animals, Cryptosporidium, and Microsporidia, suggesting that it has been lost on multiple occasions during the evolution of eukaryotes. The WLM domain is found either in stand-alone form or in association with other domains such as the RanBP2 zinc finger , the ubiquitin domain, or the PUB/PUG domain. This domain could function as a specific de-SUMOylating domain of distinct protein complexes in the nucleus and the cytoplasm []. It has been suggested to form a segregated alpha/beta structure with eight helices and five strands. Proteins containign this domain include yeast WSS1 (a weak suppressor of the Ub-related protein SMT3), and various putative metalloproteases from plant and fungal species.
Probab=100.00 E-value=8.2e-43 Score=310.01 Aligned_cols=150 Identities=56% Similarity=0.893 Sum_probs=133.2
Q ss_pred CCCCccEeeeecccCCCCCCccceecCCCcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCCCChhHHHHHHHHHH
Q 022290 1 MRKHKWKVRILSEFCPANPSLLGINIGGGAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGPHNADFYKLWDEIRK 80 (299)
Q Consensus 1 Mr~~~w~V~~L~E~~P~~~~llGlN~n~G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~H~~~F~~l~~~l~~ 80 (299)
|++|+|+|++|+||+|.+..+||+|+|+|++|.||||.+++ ..|+||+.|.+|||||||||+|++||++||+++++|..
T Consensus 33 M~~~~~~V~~L~E~~P~~~~llG~N~N~G~~I~lrLR~~~~-~~fl~~~~i~~t~lHELaH~~~~~H~~~F~~l~~~l~~ 111 (186)
T PF08325_consen 33 MRKHGWRVGSLEEFYPNGERLLGLNVNKGEKICLRLRTPDD-GGFLPYETILGTMLHELAHNVHGPHDDKFWKLLDELRK 111 (186)
T ss_pred HHHcCcccCeeeccCCCCCCCcceecCCCcEEEEEeCCCCC-CCEeeHHHHHHHHHHHHHhcccCCccHHHHHHHHHHHH
Confidence 89999999999999999999999999999999999999998 89999999999999999999999999999999999999
Q ss_pred HHHHHHHccccCCCCcccCCCCccCCCCCCCCchHHHHHHHHHHHHHhhhCCcCCCCCccccCCCCc----CCCCCHHHH
Q 022290 81 ECDELMAKGITGTGKGFDLPGRRLGGFSRQPPLSQLRQSALAAAENRARHGALLPSGPNRIGGDSSI----KAALSPIQA 156 (299)
Q Consensus 81 e~~~l~~~G~~g~g~gf~~~G~rLGG~~~~~~~~~~r~~a~~aaekr~~~~~~~~~g~~~LGg~~~~----~~~~~~re~ 156 (299)
|++.|+++||+ +||++.|++|||.....+ +.+......+.+++++|||++.. .+..++||+
T Consensus 112 e~~~l~~~G~~---~gf~~~G~~l~~~~~~~~------------~~~~~~~~~~~~~~~~LgG~s~~~~~~~~~~~~Re~ 176 (186)
T PF08325_consen 112 ECEELDAKGYT---EGFWSSGRRLGGSSGQPS------------EERELRGNGLSGGGQRLGGGSSSRPRKAQPKSPREA 176 (186)
T ss_pred HHHHHHhcCCc---cccCCCCcccCCCCcccc------------hhhhhhccccCCCCeeCCCCCCCCCCcCCCcCHHHH
Confidence 99999999998 899999999999755432 11111123366778999998752 568899999
Q ss_pred HHHHHHHHhh
Q 022290 157 AAMAAERRLH 166 (299)
Q Consensus 157 ~a~AAerR~~ 166 (299)
+|+|||||++
T Consensus 177 ~a~AAerR~~ 186 (186)
T PF08325_consen 177 AAAAAERRLR 186 (186)
T ss_pred HHHHHHhhcC
Confidence 9999999985
No 2
>KOG4842 consensus Protein involved in sister chromatid separation and/or segregation [Cell cycle control, cell division, chromosome partitioning]
Probab=99.76 E-value=7.3e-19 Score=161.57 Aligned_cols=163 Identities=30% Similarity=0.377 Sum_probs=125.3
Q ss_pred CCCCccEeeeecccCCCCCCccceecCCCcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCCCChhHHHHHHHHHH
Q 022290 1 MRKHKWKVRILSEFCPANPSLLGINIGGGAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGPHNADFYKLWDEIRK 80 (299)
Q Consensus 1 Mr~~~w~V~~L~E~~P~~~~llGlN~n~G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~H~~~F~~l~~~l~~ 80 (299)
|++|+|.|-++.++++.+.+++|+|||+|.+|.|+||...+..+|+|++++..|++|||+|++.+||+++|++.|+.|+.
T Consensus 62 mkEh~f~vti~~Dk~irnq~~sg~nvn~gski~lslr~~~~e~~~lp~e~pmgtylhel~h~lqgPhd~rfl~~L~~Lra 141 (278)
T KOG4842|consen 62 MKEHHFKVTILVDKYIRNQRLSGMNVNHGSKIMLSLRCSTDEFQFLPMECPMGTYLHELTHNLQGPHDKRFLNKLDELRA 141 (278)
T ss_pred hccccceeEEeehhHHHhhhhhccccCCcceEEEEeeccccccccccccccchhhhhhhhhhhcCCChHHHHHHHHHHhh
Confidence 89999999999999999999999999999999999997667778999999999999999999999999999999999999
Q ss_pred HHHHHHHccccCCCCcccCCCCccCCCCCCCCchHHHHHHHHHHHHHhhhCCcCCCCCccccC-------------CCCc
Q 022290 81 ECDELMAKGITGTGKGFDLPGRRLGGFSRQPPLSQLRQSALAAAENRARHGALLPSGPNRIGG-------------DSSI 147 (299)
Q Consensus 81 e~~~l~~~G~~g~g~gf~~~G~rLGG~~~~~~~~~~r~~a~~aaekr~~~~~~~~~g~~~LGg-------------~~~~ 147 (299)
+...+..+|+. .=|.+-+..|||...-. .. +. ...|.-...|...|++ -+++
T Consensus 142 d~gii~~mg~h---rW~vg~l~el~g~~nt~-v~--~~---------~tLg~stnqG~i~lrlrtdrkkgfR~y~tissT 206 (278)
T KOG4842|consen 142 DQGIIEQMGLH---RWFVGNLQELGGRANTR-VN--RY---------PTLGISTNQGVIVLRLRTDRKKGFRHYETISST 206 (278)
T ss_pred chhHHHHhccc---ceechhhhhccccccee-ec--Cc---------cceeeccccceEEEecccchhcccccCCCchHH
Confidence 99999999976 45667788888753210 00 00 0000000011112221 1122
Q ss_pred CCCCCHHHHHHHHHHHHhhhccccCCCCCCC
Q 022290 148 KAALSPIQAAAMAAERRLHDDMWCGSKSLNS 178 (299)
Q Consensus 148 ~~~~~~re~~a~AAerR~~d~~~C~~~~~~~ 178 (299)
...-.+|+++++++|++.+.+.||+-....+
T Consensus 207 l~heLtr~v~~ehde~fyrLdrql~kek~~a 237 (278)
T KOG4842|consen 207 LRHELTREVAAEHDERFYRLDRQLGKEKNNA 237 (278)
T ss_pred HHhhhhhhHhhhhhhHHHHHHHHhCcccchh
Confidence 2234578999999999999999998765444
No 3
>PF01863 DUF45: Protein of unknown function DUF45; InterPro: IPR002725 Members of this family are found in some archaebacteria, as well as Helicobacter pylori. The proteins are 190-240 amino acids long, with the C terminus being the most conserved region, containing three conserved histidines.
Probab=99.57 E-value=1.7e-15 Score=134.18 Aligned_cols=64 Identities=25% Similarity=0.306 Sum_probs=58.0
Q ss_pred CCCccceecCCCcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCCCChhHHHHHHHHHHHHHHHHH
Q 022290 18 NPSLLGINIGGGAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGPHNADFYKLWDEIRKECDELMA 87 (299)
Q Consensus 18 ~~~llGlN~n~G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~H~~~F~~l~~~l~~e~~~l~~ 87 (299)
..+.||.+ +....|.|++|+ .++|.++|+|||+|||||++|+||+++||+++.+++|+|++...
T Consensus 137 ~ksrWGsc-~~~~~I~ln~~L-----~~~P~~~idYVvvHEL~Hl~~~nHs~~Fw~~v~~~~Pd~k~~~~ 200 (205)
T PF01863_consen 137 MKSRWGSC-SSKGNITLNWRL-----VMAPPEVIDYVVVHELCHLRHPNHSKRFWALVEKYMPDYKERRK 200 (205)
T ss_pred hhhccccC-CCCCcEEeeccc-----ccCCccHHHHHHHHHHHHhccCCCCHHHHHHHHHHCcCHHHHHH
Confidence 46789999 544479999999 78999999999999999999999999999999999999998753
No 4
>COG1451 Predicted metal-dependent hydrolase [General function prediction only]
Probab=99.29 E-value=2e-12 Score=118.32 Aligned_cols=64 Identities=22% Similarity=0.280 Sum_probs=58.8
Q ss_pred CCCccceecCCCcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCCCChhHHHHHHHHHHHHHHHHH
Q 022290 18 NPSLLGINIGGGAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGPHNADFYKLWDEIRKECDELMA 87 (299)
Q Consensus 18 ~~~llGlN~n~G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~H~~~F~~l~~~l~~e~~~l~~ 87 (299)
.++.||.+.-.| .|.|++++ ..+|.+.|+||++|||||+.++||+.+||+++..++|+|+++..
T Consensus 148 ~k~~WGScs~~~-~i~~~~~l-----~~~p~~~i~YVvvHELaHLke~nHs~~Fw~lv~~~~P~~~~~~~ 211 (223)
T COG1451 148 MKRRWGSCSKAG-EIRFNWRL-----VMAPEEVIDYVVVHELAHLKEKNHSKRFWRLVEKYMPDYRAAKR 211 (223)
T ss_pred ccceeeeecCCC-cEEeehhh-----hcCCHHHHHHHHHHHHHHHhhhhccHHHHHHHHHHCCChHHHHH
Confidence 467888888888 79999999 55999999999999999999999999999999999999998764
No 5
>KOG4842 consensus Protein involved in sister chromatid separation and/or segregation [Cell cycle control, cell division, chromosome partitioning]
Probab=99.21 E-value=9.2e-12 Score=115.01 Aligned_cols=87 Identities=32% Similarity=0.426 Sum_probs=79.7
Q ss_pred CCCCccEeeeecccCCC------CCCccceecCCCcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCCCChhHHHH
Q 022290 1 MRKHKWKVRILSEFCPA------NPSLLGINIGGGAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGPHNADFYKL 74 (299)
Q Consensus 1 Mr~~~w~V~~L~E~~P~------~~~llGlN~n~G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~H~~~F~~l 74 (299)
|-.|.|.|+.|.|+.|. +..+||+|.|.| +|.+|||+.. ...|+.|+-|-.|+.|||+|+++.-|+..||+|
T Consensus 149 mg~hrW~vg~l~el~g~~nt~v~~~~tLg~stnqG-~i~lrlrtdr-kkgfR~y~tissTl~heLtr~v~~ehde~fyrL 226 (278)
T KOG4842|consen 149 MGLHRWFVGNLQELGGRANTRVNRYPTLGISTNQG-VIVLRLRTDR-KKGFRHYETISSTLRHELTREVAAEHDERFYRL 226 (278)
T ss_pred hcccceechhhhhcccccceeecCccceeeccccc-eEEEecccch-hcccccCCCchHHHHhhhhhhHhhhhhhHHHHH
Confidence 66899999999999996 367899999999 8999999965 559999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHcc
Q 022290 75 WDEIRKECDELMAKG 89 (299)
Q Consensus 75 ~~~l~~e~~~l~~~G 89 (299)
-.++-+|-..+++-+
T Consensus 227 drql~kek~~ad~~~ 241 (278)
T KOG4842|consen 227 DRQLGKEKNNADQII 241 (278)
T ss_pred HHHhCcccchhhhhc
Confidence 999999988887754
No 6
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=98.36 E-value=1.6e-07 Score=60.01 Aligned_cols=27 Identities=37% Similarity=0.903 Sum_probs=16.5
Q ss_pred CCccCCccccccccCCccccccCCCCC
Q 022290 225 QMWQCNMCTLLNQPLALTCEACGTQRN 251 (299)
Q Consensus 225 ~~W~C~~CT~~N~~~a~~C~aCgt~rp 251 (299)
+.|.|+.|++.|++.+..|.+|+++||
T Consensus 3 g~W~C~~C~~~N~~~~~~C~~C~~~rp 29 (30)
T PF00641_consen 3 GDWKCPSCTFMNPASRSKCVACGAPRP 29 (30)
T ss_dssp SSEEETTTTEEEESSSSB-TTT--BTT
T ss_pred cCccCCCCcCCchHHhhhhhCcCCCCc
Confidence 467777777777777777777776665
No 7
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=98.30 E-value=2.2e-07 Score=59.31 Aligned_cols=29 Identities=34% Similarity=0.785 Sum_probs=24.1
Q ss_pred CCCcccCCcccccCCCCccccccCCCCCC
Q 022290 257 LKGWSCKFCTLDNSSLSERCLACGEWRYS 285 (299)
Q Consensus 257 ~~~W~C~~Ct~~N~~~~~~C~~Cg~~r~~ 285 (299)
.+.|.|..|++.|+.....|.+|+++|++
T Consensus 2 ~g~W~C~~C~~~N~~~~~~C~~C~~~rp~ 30 (30)
T PF00641_consen 2 EGDWKCPSCTFMNPASRSKCVACGAPRPG 30 (30)
T ss_dssp SSSEEETTTTEEEESSSSB-TTT--BTTB
T ss_pred CcCccCCCCcCCchHHhhhhhCcCCCCcC
Confidence 56899999999999999999999999974
No 8
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=98.13 E-value=1.1e-06 Score=75.28 Aligned_cols=58 Identities=21% Similarity=0.291 Sum_probs=46.1
Q ss_pred CccceecCCCcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCC------CCChhHHHHHHHHHHH
Q 022290 20 SLLGINIGGGAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYG------PHNADFYKLWDEIRKE 81 (299)
Q Consensus 20 ~llGlN~n~G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~------~H~~~F~~l~~~l~~e 81 (299)
..+|....+...|.|+.++. .-.|.+.|++||+|||||.... +|++.|++++.++...
T Consensus 32 ~~~G~~~~~~~~I~ln~~l~----~~~~~~~l~~~l~HEm~H~~~~~~g~~~~Hg~~f~~~~~~~~~~ 95 (146)
T smart00731 32 KTGGRCLLKSAEIRLNPKLL----TENGRDRLRETLLHELCHAALYLFGRGYGHGDEWKRWMRQVNGL 95 (146)
T ss_pred hhhHHhhcCCCEEEeCHHHH----hhccHHHHHhhHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHcCC
Confidence 33565554456799998873 2368899999999999999988 9999999999888654
No 9
>KOG4198 consensus RNA-binding Ran Zn-finger protein and related proteins [General function prediction only]
Probab=98.11 E-value=1.8e-06 Score=81.49 Aligned_cols=68 Identities=24% Similarity=0.546 Sum_probs=57.6
Q ss_pred CCCCCCCccCCccccccccCCccccccCCCCCCCC------------------------------------C-------C
Q 022290 220 AVDVGQMWQCNMCTLLNQPLALTCEACGTQRNKSV------------------------------------G-------N 256 (299)
Q Consensus 220 ~~~~~~~W~C~~CT~~N~~~a~~C~aCgt~rp~~~------------------------------------~-------~ 256 (299)
.....+.|.|+.|++.|....+.|..|+.+.+... . +
T Consensus 58 ~~~~pgdw~c~~c~~~n~arr~~c~~c~~s~~~~~~~~~~~~~g~~~~~~~~r~~~~~~~~~~~~g~~~~~n~~~~r~~~ 137 (280)
T KOG4198|consen 58 DPPRPGDWNCPLCGFHNSARRLLCFRCGFSKVPLDSALTAPNSGSRSLQTGPRYFKGDWLCPRCPGLGFSRNNKPKRPWR 137 (280)
T ss_pred CCCCCcccccCccchhhHHHhhhcceecccCCCccccccCCCCcccccccccccccCCCCCCCCCCCcccccccccCCcc
Confidence 34455789999999999999999999998764211 1 5
Q ss_pred CCCcccCCcccccCCCCccccccCCCCCCCC
Q 022290 257 LKGWSCKFCTLDNSSLSERCLACGEWRYSNG 287 (299)
Q Consensus 257 ~~~W~C~~Ct~~N~~~~~~C~~Cg~~r~~~~ 287 (299)
+++|.|+.|+|+|+.....|--|+.+|+-..
T Consensus 138 ~GDW~Cp~C~fhNfarn~~C~rC~~~r~~~a 168 (280)
T KOG4198|consen 138 SGDWECPGCNFHNFARNSECFRCGAKRPLAA 168 (280)
T ss_pred ccCcccCCCCceeccccchhhhcCCcCcccc
Confidence 6899999999999999999999999998755
No 10
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=97.72 E-value=1.5e-05 Score=48.91 Aligned_cols=24 Identities=42% Similarity=0.945 Sum_probs=14.3
Q ss_pred CccCCccccccccCCccccccCCC
Q 022290 226 MWQCNMCTLLNQPLALTCEACGTQ 249 (299)
Q Consensus 226 ~W~C~~CT~~N~~~a~~C~aCgt~ 249 (299)
.|.|+.|+++|...+..|.+|+++
T Consensus 2 ~W~C~~C~~~N~~~~~~C~~C~~p 25 (26)
T smart00547 2 DWECPACTFLNFASRSKCFACGAP 25 (26)
T ss_pred cccCCCCCCcChhhhccccccCCc
Confidence 466666666666666666666543
No 11
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=97.63 E-value=2.6e-05 Score=47.89 Aligned_cols=25 Identities=36% Similarity=0.876 Sum_probs=23.6
Q ss_pred CCcccCCcccccCCCCccccccCCC
Q 022290 258 KGWSCKFCTLDNSSLSERCLACGEW 282 (299)
Q Consensus 258 ~~W~C~~Ct~~N~~~~~~C~~Cg~~ 282 (299)
+.|.|..|++.|......|.+|+++
T Consensus 1 g~W~C~~C~~~N~~~~~~C~~C~~p 25 (26)
T smart00547 1 GDWECPACTFLNFASRSKCFACGAP 25 (26)
T ss_pred CcccCCCCCCcChhhhccccccCCc
Confidence 4799999999999999999999986
No 12
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=97.35 E-value=0.00015 Score=61.74 Aligned_cols=60 Identities=23% Similarity=0.276 Sum_probs=46.0
Q ss_pred CCCCccceecCCCc---EEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCC--------CCCChhHHHHHHHHHH
Q 022290 17 ANPSLLGINIGGGA---EVKLRLRRPNREWDFFPYEQILDTMLHELCHNEY--------GPHNADFYKLWDEIRK 80 (299)
Q Consensus 17 ~~~~llGlN~n~G~---~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~--------~~H~~~F~~l~~~l~~ 80 (299)
...+.+|...-.+. .|.|+..+.. ..+.+.|..||+|||||... .+|++.|.+++.++..
T Consensus 27 ~~~~~~G~~~~~~~~~~~I~ls~~~~~----~~~~~~~~~tL~HEm~H~~~~~~~~~~~~~Hg~~fk~~~~~ig~ 97 (157)
T PF10263_consen 27 RMKRTAGRCRYKRRSPCEIRLSPKLLD----RNPEEELIDTLLHEMAHAAAYVFGGGRRRGHGKEFKQWARRIGA 97 (157)
T ss_pred CCCCceEEEEECCCCceEEEECHHHHH----hhHHHHHHHHHHHHHHHHHhhhccCCCCCCCCHHHHHHHHHHCC
Confidence 45667777544444 6888777632 26889999999999999876 7999999998887744
No 13
>PF12773 DZR: Double zinc ribbon
Probab=97.12 E-value=0.00049 Score=48.28 Aligned_cols=50 Identities=28% Similarity=0.535 Sum_probs=44.2
Q ss_pred CCccccccccCCccccccCCCCCCCCCCCCCcccCCcccccCCCCccccccC
Q 022290 229 CNMCTLLNQPLALTCEACGTQRNKSVGNLKGWSCKFCTLDNSSLSERCLACG 280 (299)
Q Consensus 229 C~~CT~~N~~~a~~C~aCgt~rp~~~~~~~~W~C~~Ct~~N~~~~~~C~~Cg 280 (299)
|+.|...|+..+..|..|+++-+. .....+.|+.|...|...+..|..||
T Consensus 1 Cp~Cg~~~~~~~~fC~~CG~~l~~--~~~~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPHCGTPLPP--PDQSKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred CCCcCCcCCccccCChhhcCChhh--ccCCCCCCcCCcCCCcCCcCccCccc
Confidence 899999999999999999988661 23457999999999999999999997
No 14
>KOG4198 consensus RNA-binding Ran Zn-finger protein and related proteins [General function prediction only]
Probab=97.09 E-value=0.00041 Score=65.78 Aligned_cols=32 Identities=25% Similarity=0.503 Sum_probs=29.7
Q ss_pred CCCCCCccCCccccccccCCccccccCCCCCC
Q 022290 221 VDVGQMWQCNMCTLLNQPLALTCEACGTQRNK 252 (299)
Q Consensus 221 ~~~~~~W~C~~CT~~N~~~a~~C~aCgt~rp~ 252 (299)
+...+.|.|+.|+|+|......|-.|+.+|+.
T Consensus 135 ~~~~GDW~Cp~C~fhNfarn~~C~rC~~~r~~ 166 (280)
T KOG4198|consen 135 PWRSGDWECPGCNFHNFARNSECFRCGAKRPL 166 (280)
T ss_pred CccccCcccCCCCceeccccchhhhcCCcCcc
Confidence 46778999999999999999999999999986
No 15
>KOG4477 consensus RING1 interactor RYBP and related Zn-finger-containing proteins [Transcription]
Probab=96.14 E-value=0.0028 Score=56.82 Aligned_cols=34 Identities=29% Similarity=0.704 Sum_probs=28.7
Q ss_pred CCCCCCCccCCccccccccCCccccccCCCCCCC
Q 022290 220 AVDVGQMWQCNMCTLLNQPLALTCEACGTQRNKS 253 (299)
Q Consensus 220 ~~~~~~~W~C~~CT~~N~~~a~~C~aCgt~rp~~ 253 (299)
...+.+.|.|..|||.|.+.+-.|.+|+..+..+
T Consensus 18 p~~Deg~WdCsvCTFrNsAeAfkC~vCdvRKGTS 51 (228)
T KOG4477|consen 18 PNDDEGKWDCSVCTFRNSAEAFKCFVCDVRKGTS 51 (228)
T ss_pred CccccCceeeeeeeecchhhhhheeeeccccccc
Confidence 3456689999999999999999999999876544
No 16
>PRK04351 hypothetical protein; Provisional
Probab=96.00 E-value=0.0071 Score=52.50 Aligned_cols=46 Identities=22% Similarity=0.537 Sum_probs=33.4
Q ss_pred CcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhc------C-CCCCChhHHHHHHHH
Q 022290 29 GAEVKLRLRRPNREWDFFPYEQILDTMLHELCHN------E-YGPHNADFYKLWDEI 78 (299)
Q Consensus 29 G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~------~-~~~H~~~F~~l~~~l 78 (299)
...|.|+-..- .-.+.+.|..||.|||||+ . +.+|+++|..++.++
T Consensus 43 ~~~I~lnp~ll----~~~~~~~l~~vv~HElcH~~~~~~g~g~~h~g~~fk~~~~~v 95 (149)
T PRK04351 43 DHHIEFNPKML----EEYGLEELIGIIKHELCHYHLHLEGKGYQHRDRDFKELLKQV 95 (149)
T ss_pred CCeEEeCHHHH----hhccHHHHHhhHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHh
Confidence 34577765542 1245789999999999998 2 567888998877765
No 17
>KOG4477 consensus RING1 interactor RYBP and related Zn-finger-containing proteins [Transcription]
Probab=95.95 E-value=0.0022 Score=57.51 Aligned_cols=32 Identities=25% Similarity=0.692 Sum_probs=27.7
Q ss_pred CCCCCcccCCcccccCCCCccccccCCCCCCC
Q 022290 255 GNLKGWSCKFCTLDNSSLSERCLACGEWRYSN 286 (299)
Q Consensus 255 ~~~~~W~C~~Ct~~N~~~~~~C~~Cg~~r~~~ 286 (299)
...+.|.|++|||.|.+.+.+|.+|+..+--+
T Consensus 20 ~Deg~WdCsvCTFrNsAeAfkC~vCdvRKGTS 51 (228)
T KOG4477|consen 20 DDEGKWDCSVCTFRNSAEAFKCFVCDVRKGTS 51 (228)
T ss_pred cccCceeeeeeeecchhhhhheeeeccccccc
Confidence 34678999999999999999999999877543
No 18
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=95.93 E-value=0.0062 Score=64.02 Aligned_cols=50 Identities=24% Similarity=0.504 Sum_probs=44.1
Q ss_pred cCCccccccccCCccccccCCCCCCCCCCCCCcccCCcccccCCCCccccccCCCCC
Q 022290 228 QCNMCTLLNQPLALTCEACGTQRNKSVGNLKGWSCKFCTLDNSSLSERCLACGEWRY 284 (299)
Q Consensus 228 ~C~~CT~~N~~~a~~C~aCgt~rp~~~~~~~~W~C~~Ct~~N~~~~~~C~~Cg~~r~ 284 (299)
.|+.|...|+..+..|..||++-.. -.|+.|+..|......|..||+.-.
T Consensus 3 ~Cp~Cg~~n~~~akFC~~CG~~l~~-------~~Cp~CG~~~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 3 ICPQCQFENPNNNRFCQKCGTSLTH-------KPCPQCGTEVPVDEAHCPNCGAETG 52 (645)
T ss_pred cCCCCCCcCCCCCccccccCCCCCC-------CcCCCCCCCCCcccccccccCCccc
Confidence 6999999999999999999987421 3699999999999999999999643
No 19
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=95.40 E-value=0.013 Score=51.00 Aligned_cols=33 Identities=27% Similarity=0.441 Sum_probs=27.5
Q ss_pred CHHHHHHHHHHHhhhcC-------CCCCChhHHHHHHHHH
Q 022290 47 PYEQILDTMLHELCHNE-------YGPHNADFYKLWDEIR 79 (299)
Q Consensus 47 p~~~i~~v~lHELaH~~-------~~~H~~~F~~l~~~l~ 79 (299)
-.+.|+.||.|||||+. +.+|+++|-.+|.++.
T Consensus 57 ~~~f~~~vV~HELaHl~ly~~~gr~~phg~ewk~lm~qV~ 96 (156)
T COG3091 57 GEDFIEQVVPHELAHLHLYQEFGRYKPHGKEWKLLMQQVL 96 (156)
T ss_pred cHHHHHHHHHHHHHHHHHHHHcCCCCCCchhHHHHHHHhC
Confidence 34679999999999985 5699999998887764
No 20
>PRK04860 hypothetical protein; Provisional
Probab=94.89 E-value=0.018 Score=50.63 Aligned_cols=46 Identities=22% Similarity=0.267 Sum_probs=32.7
Q ss_pred CcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcC-C------CCCChhHHHHHHHH
Q 022290 29 GAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNE-Y------GPHNADFYKLWDEI 78 (299)
Q Consensus 29 G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~-~------~~H~~~F~~l~~~l 78 (299)
...|.||-..- .-.+.+.|..||.|||||++ | .+|+++|-.++.++
T Consensus 45 ~~~I~~Np~ll----~~~~~~~l~~~v~HEl~H~~~~~~~g~~~~Hg~ewk~lm~~v 97 (160)
T PRK04860 45 SNEIRLNPVLL----LENQQAFIDEVVPHELAHLLVYQLFGRVAPHGKEWQWMMESV 97 (160)
T ss_pred cCCeeeCHHHH----hhCcHHHHHhHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHh
Confidence 34466664442 22477899999999999975 1 38998888887764
No 21
>KOG4345 consensus NF-kappa B regulator AP20/Cezanne [Signal transduction mechanisms]
Probab=94.32 E-value=0.0048 Score=64.48 Aligned_cols=60 Identities=15% Similarity=0.242 Sum_probs=51.0
Q ss_pred CCCccCCccccccccCCccccccCCCCCCCC-------------------------------------------------
Q 022290 224 GQMWQCNMCTLLNQPLALTCEACGTQRNKSV------------------------------------------------- 254 (299)
Q Consensus 224 ~~~W~C~~CT~~N~~~a~~C~aCgt~rp~~~------------------------------------------------- 254 (299)
...|.|..|++.|-+.+++|.+|...++...
T Consensus 5 ~~~W~~~~~~~~~lp~al~lS~~~~s~~~~~~l~eDifk~~n~~~~~~~sd~~~~r~v~~~~~~p~f~~s~~~r~~~~~s 84 (774)
T KOG4345|consen 5 AEKWACELCDYMTLPMALVLSDFRRSTGAEPGLAEDIFKGKNWDIHAALSDYEQLRQVHEMNLTPSFCESGQPREIIHKS 84 (774)
T ss_pred hHHHHHHhhccccCchhhHHHHHHhccCCCCCcchhhccCCCccceeecccHHHHHhhhccCCCCcccccCCcccccccc
Confidence 3579999999999999999999987766321
Q ss_pred --CCCCCcccCCcccccCCCCccccccCCCC
Q 022290 255 --GNLKGWSCKFCTLDNSSLSERCLACGEWR 283 (299)
Q Consensus 255 --~~~~~W~C~~Ct~~N~~~~~~C~~Cg~~r 283 (299)
....+|.|+.|+++||+...+|+.|-+.+
T Consensus 85 ~~~~~~k~~~~~~~~lnw~re~R~~~~ls~~ 115 (774)
T KOG4345|consen 85 LIDRNIKWPRPSLQRLNWPREKRLSRGLSHA 115 (774)
T ss_pred cccccccCCchHhhhhhHHHHHHHHHHhhcc
Confidence 12457999999999999999999998766
No 22
>KOG4345 consensus NF-kappa B regulator AP20/Cezanne [Signal transduction mechanisms]
Probab=92.73 E-value=0.056 Score=56.82 Aligned_cols=68 Identities=12% Similarity=-0.001 Sum_probs=54.5
Q ss_pred CCCCCCCccCCccccccccCCccccccCCCCCCCC--------------------------------CC-----------
Q 022290 220 AVDVGQMWQCNMCTLLNQPLALTCEACGTQRNKSV--------------------------------GN----------- 256 (299)
Q Consensus 220 ~~~~~~~W~C~~CT~~N~~~a~~C~aCgt~rp~~~--------------------------------~~----------- 256 (299)
......+|+|+.|+++|.+....|..|-+.+.... ..
T Consensus 85 ~~~~~~k~~~~~~~~lnw~re~R~~~~ls~~gd~~~~~~q~pq~s~~~qs~~VaL~~~l~~~l~~~dt~~~N~l~w~~h~ 164 (774)
T KOG4345|consen 85 LIDRNIKWPRPSLQRLNWPREKRLSRGLSHAGDMPILAFQLPQLSVYEQSTPVALEKALFRLLPLADTGDGNCLMWGFHD 164 (774)
T ss_pred cccccccCCchHhhhhhHHHHHHHHHHhhccCCCccchhccchhhccccccchhhhhhhhhcccccccCCccchhhhhhh
Confidence 46677899999999999999999999976652110 00
Q ss_pred ------------------CCCcccCCcccccCCCCccccccCCCCCCCC
Q 022290 257 ------------------LKGWSCKFCTLDNSSLSERCLACGEWRYSNG 287 (299)
Q Consensus 257 ------------------~~~W~C~~Ct~~N~~~~~~C~~Cg~~r~~~~ 287 (299)
...|.|..|++.|++...+|.+|++.+....
T Consensus 165 lvlqk~l~t~l~~~~~rw~~eW~~lik~ass~pr~~r~~~~~~~~~~e~ 213 (774)
T KOG4345|consen 165 LVLQKALYTGLCYGTERWNDEWTELIKLASSEPRMHRSGNGGTGGGVEI 213 (774)
T ss_pred HHHHHHHHHhhchhhHHHHHHHHHHHHhhcccchhhhcccCCCCCCccc
Confidence 1249999999999999999999999887654
No 23
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=91.97 E-value=0.12 Score=40.88 Aligned_cols=39 Identities=18% Similarity=0.235 Sum_probs=26.8
Q ss_pred ceecCCCcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCCCC
Q 022290 23 GINIGGGAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGPHN 68 (299)
Q Consensus 23 GlN~n~G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~H~ 68 (299)
|+..-....|.+++.. .+.+.+..|++|||+|.++....
T Consensus 4 G~~~~~~~~i~~~~~~-------~~~~~~~~~l~HE~~H~~~~~~~ 42 (128)
T PF13485_consen 4 GVYYPGFNRIVVYFQG-------SDEDWLDRVLAHELAHQWFGNYF 42 (128)
T ss_pred EEEecCCCEEEEecCC-------CCHHHHHHHHHHHHHHHHHHHHc
Confidence 4444444566665543 56677889999999999876543
No 24
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=90.34 E-value=0.16 Score=32.94 Aligned_cols=26 Identities=19% Similarity=0.441 Sum_probs=18.1
Q ss_pred CcccCCcccccCC--CCccccccCCCCC
Q 022290 259 GWSCKFCTLDNSS--LSERCLACGEWRY 284 (299)
Q Consensus 259 ~W~C~~Ct~~N~~--~~~~C~~Cg~~r~ 284 (299)
.|.|..|+|.-.. ..+.|..|+.++.
T Consensus 1 ~~~C~~CGy~y~~~~~~~~CP~Cg~~~~ 28 (33)
T cd00350 1 KYVCPVCGYIYDGEEAPWVCPVCGAPKD 28 (33)
T ss_pred CEECCCCCCEECCCcCCCcCcCCCCcHH
Confidence 3788888876444 3678888887653
No 25
>PF06114 DUF955: Domain of unknown function (DUF955); InterPro: IPR010359 This is a family of bacterial and viral proteins with undetermined function. A conserved H-E-X-X-H motif is suggestive of a catalytic active site and shows similarity to IPR001915 from INTERPRO.; PDB: 3DTE_A 3DTK_A 3DTI_A.
Probab=90.29 E-value=0.37 Score=37.67 Aligned_cols=58 Identities=21% Similarity=0.100 Sum_probs=34.8
Q ss_pred ccceecCC--CcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCCCChhHHHHHHHHHHHHHHHH
Q 022290 21 LLGINIGG--GAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGPHNADFYKLWDEIRKECDELM 86 (299)
Q Consensus 21 llGlN~n~--G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~H~~~F~~l~~~l~~e~~~l~ 86 (299)
+.|..... ...|.|+-+. +...-..+++|||.|.+...+...++........+..+..
T Consensus 18 ~~~~~~~~~~~~~I~in~~~--------~~~~~~f~laHELgH~~~~~~~~~~~~~~~~~~~~~~E~~ 77 (122)
T PF06114_consen 18 LGGFSIPKENNPIIFINSNL--------SPERQRFTLAHELGHILLHHGDETFNYYLNYFFNERQERE 77 (122)
T ss_dssp EEEETT----TTEEEEESSS---------HHHHHHHHHHHHHHHHHHH-HHHHHHHHHH--THHHHHH
T ss_pred cCEEEEecCcCCEEEECCCC--------CHHHHHHHHHHHHHHHHhhhccccchhhccccchhhHHHH
Confidence 44444443 5678887664 4577789999999999988888765444444444444433
No 26
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=89.62 E-value=0.21 Score=30.76 Aligned_cols=23 Identities=22% Similarity=0.473 Sum_probs=14.2
Q ss_pred cccCCcccccCCCCccccccCCC
Q 022290 260 WSCKFCTLDNSSLSERCLACGEW 282 (299)
Q Consensus 260 W~C~~Ct~~N~~~~~~C~~Cg~~ 282 (299)
+.|+.|+..|......|..||++
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCcccccChhhCCC
Confidence 45666666666666666666653
No 27
>PF04450 BSP: Peptidase of plants and bacteria; InterPro: IPR007541 These basic secretory proteins (BSPs) are believed to be part of the plants defence mechanism against pathogens [].
Probab=89.12 E-value=0.24 Score=45.19 Aligned_cols=57 Identities=18% Similarity=0.100 Sum_probs=42.5
Q ss_pred cEEEEEecCCCCCCC-CCCHHHHHHHHHHHhhhcCC-CCCChhHHHHHHHHHHHHHHHHH
Q 022290 30 AEVKLRLRRPNREWD-FFPYEQILDTMLHELCHNEY-GPHNADFYKLWDEIRKECDELMA 87 (299)
Q Consensus 30 ~~I~LrLR~~~~~~~-f~p~~~i~~v~lHELaH~~~-~~H~~~F~~l~~~l~~e~~~l~~ 87 (299)
.+|.|.++.-.+... -.....|..||.|||+|++. .+++..++-|++-+. +|..|.+
T Consensus 74 ~~I~~S~~~i~~~~~~~~~~~Ei~Gvl~HE~~H~~Q~~~~~~~P~~liEGIA-DyVRl~a 132 (205)
T PF04450_consen 74 KEIHFSARYIAKYPADGDVRDEIIGVLYHEMVHCWQWDGRGTAPGGLIEGIA-DYVRLKA 132 (205)
T ss_pred cEEEEeHHHHhhcccccchHHHHHHHHHHHHHHHhhcCCCCCCChhheecHH-HHHHHHc
Confidence 789999988653211 12236899999999999997 458899999988775 4666665
No 28
>COG4219 MecR1 Antirepressor regulating drug resistance, predicted signal transduction N-terminal membrane component [Transcription / Signal transduction mechanisms]
Probab=88.30 E-value=0.27 Score=47.85 Aligned_cols=29 Identities=28% Similarity=0.326 Sum_probs=23.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhhcCCCC
Q 022290 38 RPNREWDFFPYEQILDTMLHELCHNEYGP 66 (299)
Q Consensus 38 ~~~~~~~f~p~~~i~~v~lHELaH~~~~~ 66 (299)
.|.|-..-++.|.++|+++|||.|+.+++
T Consensus 177 lP~d~~~r~~~ee~~yIilHEl~Hlk~gD 205 (337)
T COG4219 177 LPADFVERLTDEELKYIILHELSHLKRGD 205 (337)
T ss_pred ccHHHHhhcCHHhhhhhHhHHHhhhhccc
Confidence 34444456788999999999999999875
No 29
>PF08325 WLM: WLM domain; InterPro: IPR013536 The WLM (WSS1-like metalloprotease) domain is a globular domain related to the zincin-like superfamily of Zn-dependent peptidase. Since the WLM domain contains all known active site residues of zincins, it is predicted to be a catalytically active peptidase domain. The WLM domain is a eukaryotic domain represented in plants, fungi, Plasmodium, and kinetoplastids. By contrast, it is absent in animals, Cryptosporidium, and Microsporidia, suggesting that it has been lost on multiple occasions during the evolution of eukaryotes. The WLM domain is found either in stand-alone form or in association with other domains such as the RanBP2 zinc finger , the ubiquitin domain, or the PUB/PUG domain. This domain could function as a specific de-SUMOylating domain of distinct protein complexes in the nucleus and the cytoplasm []. It has been suggested to form a segregated alpha/beta structure with eight helices and five strands. Proteins containign this domain include yeast WSS1 (a weak suppressor of the Ub-related protein SMT3), and various putative metalloproteases from plant and fungal species.
Probab=88.17 E-value=1.2 Score=39.98 Aligned_cols=79 Identities=28% Similarity=0.323 Sum_probs=53.7
Q ss_pred HHHHHHHHHHhhhcCCCCCChhHHHHHHHHHHHHHHH------HHcccc-C------------CCCcccCCCCccCCCCC
Q 022290 49 EQILDTMLHELCHNEYGPHNADFYKLWDEIRKECDEL------MAKGIT-G------------TGKGFDLPGRRLGGFSR 109 (299)
Q Consensus 49 ~~i~~v~lHELaH~~~~~H~~~F~~l~~~l~~e~~~l------~~~G~~-g------------~g~gf~~~G~rLGG~~~ 109 (299)
..+..=|.| ..|--|..---++|+.|.+-..+.+.- ...|-. | ...++.+.|++|||.+.
T Consensus 84 ~t~lHELaH-~~~~~H~~~F~~l~~~l~~e~~~l~~~G~~~gf~~~G~~l~~~~~~~~~~~~~~~~~~~~~~~~LgG~s~ 162 (186)
T PF08325_consen 84 GTMLHELAH-NVHGPHDDKFWKLLDELRKECEELDAKGYTEGFWSSGRRLGGSSGQPSEERELRGNGLSGGGQRLGGGSS 162 (186)
T ss_pred HHHHHHHHh-cccCCccHHHHHHHHHHHHHHHHHHhcCCccccCCCCcccCCCCcccchhhhhhccccCCCCeeCCCCCC
Confidence 456677888 458888888888888888777766663 222211 0 01235567899999765
Q ss_pred C----CCchHHHHHHHHHHHHHh
Q 022290 110 Q----PPLSQLRQSALAAAENRA 128 (299)
Q Consensus 110 ~----~~~~~~r~~a~~aaekr~ 128 (299)
. ....+.|+.+++||++|.
T Consensus 163 ~~~~~~~~~~~Re~~a~AAerR~ 185 (186)
T PF08325_consen 163 SRPRKAQPKSPREAAAAAAERRL 185 (186)
T ss_pred CCCCcCCCcCHHHHHHHHHHhhc
Confidence 2 345568899999999985
No 30
>PF05569 Peptidase_M56: BlaR1 peptidase M56; InterPro: IPR008756 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M56 (clan M-). The predicted active site residues for members of this family occur in the motif HEXXH. The type example is BlaR1 peptidase from Bacillus licheniformis. Production of beta-Lactamase and penicillin-binding protein 2a (which mediate staphylococcal resistance to beta-lactam antibiotics) is regulated by a signal-transducing integral membrane protein and a transcriptional repressor. The signal transducer is a fusion protein with penicillin-binding and zinc metalloprotease domains. The signal for protein expression is transmitted by site-specific proteolytic cleavage of both the transducer, which auto-activates, and the repressor, which is inactivated, unblocking gene transcription.
Probab=87.81 E-value=0.84 Score=42.91 Aligned_cols=26 Identities=23% Similarity=0.264 Sum_probs=21.0
Q ss_pred CCHHHHHHHHHHHhhhcCCCCCChhH
Q 022290 46 FPYEQILDTMLHELCHNEYGPHNADF 71 (299)
Q Consensus 46 ~p~~~i~~v~lHELaH~~~~~H~~~F 71 (299)
+..+.+++++.|||+|+.+++.=.+|
T Consensus 191 ~~~~el~~il~HEl~Hikr~D~~~~~ 216 (299)
T PF05569_consen 191 LSEEELRAILLHELAHIKRRDLLWKL 216 (299)
T ss_pred cCHHHHHHHHHHHHHHHHCCChHHHH
Confidence 56689999999999999988754433
No 31
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=87.21 E-value=0.37 Score=29.66 Aligned_cols=24 Identities=29% Similarity=0.555 Sum_probs=21.6
Q ss_pred CccCCccccccccCCccccccCCC
Q 022290 226 MWQCNMCTLLNQPLALTCEACGTQ 249 (299)
Q Consensus 226 ~W~C~~CT~~N~~~a~~C~aCgt~ 249 (299)
...|+.|...|...+..|..||++
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGAK 25 (26)
T ss_pred cCCCcccCCcCCcccccChhhCCC
Confidence 468999999999999999999965
No 32
>KOG3931 consensus Uncharacterized conserved protein [Function unknown]
Probab=87.14 E-value=1 Score=44.42 Aligned_cols=55 Identities=29% Similarity=0.474 Sum_probs=42.2
Q ss_pred ceecC--CCcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcC---------CCCCChhHHHHHHHHH
Q 022290 23 GINIG--GGAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNE---------YGPHNADFYKLWDEIR 79 (299)
Q Consensus 23 GlN~n--~G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~---------~~~H~~~F~~l~~~l~ 79 (299)
|++.- +|.-..|||-.| -...+|...++.||||||.|-. ...|...|-+.+..+.
T Consensus 77 GICsyeg~gg~csIRLSeP--LLkLRPRkDLVETLLHEMIHAYlFV~n~~~dr~GHGP~F~~hMhrIN 142 (484)
T KOG3931|consen 77 GICSYEGKGGMCSIRLSEP--LLKLRPRKDLVETLLHEMIHAYLFVTNNDKDREGHGPEFCKHMHRIN 142 (484)
T ss_pred ceeeeccccceEEEEecch--hhccCchHHHHHHHHHHHHHHheeEecccccCCCCChHHHHHHHHHh
Confidence 44433 355678888775 3467899999999999999953 3579999999988764
No 33
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=87.01 E-value=0.63 Score=43.20 Aligned_cols=58 Identities=24% Similarity=0.189 Sum_probs=39.3
Q ss_pred ccEeeeecccCCCCCCccceecCCCcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCCCC
Q 022290 5 KWKVRILSEFCPANPSLLGINIGGGAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGPHN 68 (299)
Q Consensus 5 ~w~V~~L~E~~P~~~~llGlN~n~G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~H~ 68 (299)
.|+|..+..-.| |.=.+|.+.+.+ +|-|.--+- ..+..++|..||.||++|+++.+.=
T Consensus 117 ~~~v~i~~~~~~-NAFa~g~~~~~~-~V~vt~gLl----~~l~~dEl~aVlaHElgHi~~rd~~ 174 (302)
T COG0501 117 MPEVYILETPQP-NAFALGGGPKNG-RVVVTTGLL----DLLNDDELEAVLAHELGHIKNRHTL 174 (302)
T ss_pred CCeeEEecCCCc-cceecCCCCCCe-eEEecHHHH----hhCCHHHHHHHHHHHHHHHhcccHH
Confidence 466666653333 444555555444 577766653 2578899999999999999987654
No 34
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=86.94 E-value=0.37 Score=29.04 Aligned_cols=21 Identities=24% Similarity=0.550 Sum_probs=14.1
Q ss_pred cCCcccccCCCCccccccCCC
Q 022290 262 CKFCTLDNSSLSERCLACGEW 282 (299)
Q Consensus 262 C~~Ct~~N~~~~~~C~~Cg~~ 282 (299)
|+.|+..+......|..||++
T Consensus 2 Cp~CG~~~~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCPNCGTP 22 (23)
T ss_pred CcccCCCCCCcCcchhhhCCc
Confidence 666666666666667776654
No 35
>cd04270 ZnMc_TACE_like Zinc-dependent metalloprotease; TACE_like subfamily. TACE, the tumor-necrosis factor-alpha converting enzyme, releases soluble TNF-alpha from transmembrane pro-TNF-alpha.
Probab=86.80 E-value=0.53 Score=43.59 Aligned_cols=27 Identities=33% Similarity=0.367 Sum_probs=23.5
Q ss_pred CCCHHHHHHHHHHHhhhcCCCCCChhH
Q 022290 45 FFPYEQILDTMLHELCHNEYGPHNADF 71 (299)
Q Consensus 45 f~p~~~i~~v~lHELaH~~~~~H~~~F 71 (299)
..|+..+..||+|||-|+.-++||..-
T Consensus 161 ~~~~~~~a~t~AHElGHnlGm~HD~~~ 187 (244)
T cd04270 161 RVPTKESDLVTAHELGHNFGSPHDPDI 187 (244)
T ss_pred ccchhHHHHHHHHHHHHhcCCCCCCCC
Confidence 457777889999999999999999864
No 36
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=86.47 E-value=0.38 Score=31.61 Aligned_cols=26 Identities=27% Similarity=0.701 Sum_probs=18.8
Q ss_pred CcccCCcccccCCC--CccccccCCCCC
Q 022290 259 GWSCKFCTLDNSSL--SERCLACGEWRY 284 (299)
Q Consensus 259 ~W~C~~Ct~~N~~~--~~~C~~Cg~~r~ 284 (299)
.|.|..|++.-... -..|.+|+.++.
T Consensus 2 ~~~C~~CG~i~~g~~~p~~CP~Cg~~~~ 29 (34)
T cd00729 2 VWVCPVCGYIHEGEEAPEKCPICGAPKE 29 (34)
T ss_pred eEECCCCCCEeECCcCCCcCcCCCCchH
Confidence 48888888875443 468888888653
No 37
>PRK02870 heat shock protein HtpX; Provisional
Probab=85.54 E-value=0.92 Score=44.36 Aligned_cols=44 Identities=20% Similarity=0.206 Sum_probs=29.6
Q ss_pred CCCccceecCCCcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCC
Q 022290 18 NPSLLGINIGGGAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGP 66 (299)
Q Consensus 18 ~~~llGlN~n~G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~ 66 (299)
|.=.+|.+.+.+ .|.|.--+- ..++.+.|..||.|||+|+.|++
T Consensus 145 NAFA~G~~~~~~-~Ivvt~GLL----~~L~~dEL~aVlAHELgHik~~d 188 (336)
T PRK02870 145 NAFASGYSEKSA-MVAITTGLL----EKLDRDELQAVMAHELSHIRHGD 188 (336)
T ss_pred ceEEecCCCCCc-EEEEehHHh----hhCCHHHHHHHHHHHHHHHHccc
Confidence 444556554444 466654442 23688999999999999997754
No 38
>PRK04897 heat shock protein HtpX; Provisional
Probab=85.51 E-value=0.53 Score=44.94 Aligned_cols=43 Identities=14% Similarity=0.075 Sum_probs=28.0
Q ss_pred ccceecCCCcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCCCC
Q 022290 21 LLGINIGGGAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGPHN 68 (299)
Q Consensus 21 llGlN~n~G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~H~ 68 (299)
..|.+.+++ .|.+.--+- ..++.++|..||.|||+|+.|++.-
T Consensus 112 a~G~~~~~~-~v~vt~gLl----~~l~~~El~aVlAHElgHi~~~d~~ 154 (298)
T PRK04897 112 ATGSSPKNA-AVAVTTGLL----AIMNREELEGVIGHEISHIRNYDIR 154 (298)
T ss_pred EeccCCCCc-EEEeehHHH----hhCCHHHHHHHHHHHHHHHhcCCHH
Confidence 344444333 455553221 2367899999999999999977653
No 39
>PRK03072 heat shock protein HtpX; Provisional
Probab=85.48 E-value=0.54 Score=44.68 Aligned_cols=24 Identities=17% Similarity=0.101 Sum_probs=20.8
Q ss_pred CCCHHHHHHHHHHHhhhcCCCCCC
Q 022290 45 FFPYEQILDTMLHELCHNEYGPHN 68 (299)
Q Consensus 45 f~p~~~i~~v~lHELaH~~~~~H~ 68 (299)
.++.++|..||.|||+|+.+++--
T Consensus 121 ~l~~~El~aVlAHElgHi~~~d~~ 144 (288)
T PRK03072 121 ILNERELRGVLGHELSHVYNRDIL 144 (288)
T ss_pred hCCHHHHHHHHHHHHHHHhcCCHH
Confidence 468899999999999999987643
No 40
>PF12388 Peptidase_M57: Dual-action HEIGH metallo-peptidase; InterPro: IPR024653 This entry represents the metallopeptidases M10, M27 and M57. The catalytic triad for proteases in this entry is HE-H-H, which in many members is in the sequence motif HEIGH [].
Probab=84.33 E-value=1.1 Score=41.10 Aligned_cols=41 Identities=17% Similarity=0.085 Sum_probs=30.7
Q ss_pred ecCCCcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCCCChhH
Q 022290 25 NIGGGAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGPHNADF 71 (299)
Q Consensus 25 N~n~G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~H~~~F 71 (299)
|-+.+..|.| .-. .-.....+..||.|||-|.+-.-|.+-|
T Consensus 113 ~G~P~~~I~I-~~~-----~~~~~~~~~hvi~HEiGH~IGfRHTD~~ 153 (211)
T PF12388_consen 113 NGNPYKFIQI-YGL-----SNYSVNVIEHVITHEIGHCIGFRHTDYF 153 (211)
T ss_pred CCCCCceEEE-Eec-----CCCchhHHHHHHHHHhhhhccccccCcC
Confidence 3344667888 322 3467788999999999999999998733
No 41
>PRK03982 heat shock protein HtpX; Provisional
Probab=84.21 E-value=0.65 Score=43.95 Aligned_cols=44 Identities=14% Similarity=0.095 Sum_probs=28.9
Q ss_pred ccceecCCCcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCCCCh
Q 022290 21 LLGINIGGGAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGPHNA 69 (299)
Q Consensus 21 llGlN~n~G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~H~~ 69 (299)
.+|...+++ .|.|.--+- ..++.++|..||.|||.|+.|++.-.
T Consensus 100 a~G~~~~~~-~V~vt~gLl----~~l~~~El~AVlAHElgHi~~~h~~~ 143 (288)
T PRK03982 100 ATGRDPKHA-VVAVTEGIL----NLLNEDELEGVIAHELTHIKNRDTLI 143 (288)
T ss_pred EeccCCCCe-EEEeehHHH----hhCCHHHHHHHHHHHHHHHHcCCHHH
Confidence 445544343 354443332 23578999999999999999987433
No 42
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=83.53 E-value=1.1 Score=50.32 Aligned_cols=54 Identities=19% Similarity=0.374 Sum_probs=42.3
Q ss_pred CccCCccccccccCCccccccCCCCCCCCCCCCCcccCCcccccCCC---CccccccCCCCCCCC
Q 022290 226 MWQCNMCTLLNQPLALTCEACGTQRNKSVGNLKGWSCKFCTLDNSSL---SERCLACGEWRYSNG 287 (299)
Q Consensus 226 ~W~C~~CT~~N~~~a~~C~aCgt~rp~~~~~~~~W~C~~Ct~~N~~~---~~~C~~Cg~~r~~~~ 287 (299)
.-.|+.|.-..+. ..|..||.... ..+.|+.|....... +..|.-|+++..+..
T Consensus 667 ~rkCPkCG~~t~~--~fCP~CGs~te------~vy~CPsCGaev~~des~a~~CP~CGtplv~~~ 723 (1337)
T PRK14714 667 RRRCPSCGTETYE--NRCPDCGTHTE------PVYVCPDCGAEVPPDESGRVECPRCDVELTPYQ 723 (1337)
T ss_pred EEECCCCCCcccc--ccCcccCCcCC------CceeCccCCCccCCCccccccCCCCCCcccccc
Confidence 3799999998765 39999997742 257999999976554 779999998876544
No 43
>PF01435 Peptidase_M48: Peptidase family M48 This is family M48 in the peptidase classification. ; InterPro: IPR001915 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M48 (Ste24 endopeptidase family, clan M-); members of both subfamily are represented. The members of this set of proteins are mostly described as probable protease htpX homologue (3.4.24 from EC) or CAAX prenyl protease 1, which proteolytically removes the C-terminal three residues of farnesylated proteins. They are integral membrane proteins associated with the endoplasmic reticulum and Golgi, binding one zinc ion per subunit. In Saccharomyces cerevisiae (Baker's yeast) Ste24p is required for the first NH2-terminal proteolytic processing event within the a-factor precursor, which takes place after COOH-terminal CAAX modification is complete. The Ste24p contains multiple predicted membrane spans, a zinc metalloprotease motif (HEXXH), and a COOH-terminal ER retrieval signal (KKXX). The HEXXH protease motif is critical for Ste24p activity, since Ste24p fails to function when conserved residues within this motif are mutated. The Ste24p homologues occur in a diverse group of organisms, including Escherichia coli, Schizosaccharomyces pombe (Fission yeast), Haemophilus influenzae, and Homo sapiens (Human), which indicates that the gene is highly conserved throughout evolution. Ste24p and the proteins related to it define a subfamily of proteins that are likely to function as intracellular, membrane-associated zinc metalloproteases []. HtpX is a zinc-dependent endoprotease member of the membrane-localized proteolytic system in E. coli, which participates in the proteolytic quality control of membrane proteins in conjunction with FtsH, a membrane-bound and ATP-dependent protease. Biochemical characterisation revealed that HtpX undergoes self-degradation upon cell disruption or membrane solubilization. It can also degraded casein and cleaves solubilized membrane proteins, for example, SecY []. Expression of HtpX in the plasma membrane is under the control of CpxR, with the metalloproteinase active site of HtpX located on the cytosolic side of the membrane. This suggests a potential role for HtpX in the response to mis-folded proteins [].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis, 0016020 membrane; PDB: 3CQB_A 3C37_B.
Probab=83.20 E-value=0.6 Score=41.22 Aligned_cols=38 Identities=11% Similarity=0.072 Sum_probs=29.1
Q ss_pred CcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCCCChh
Q 022290 29 GAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGPHNAD 70 (299)
Q Consensus 29 G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~H~~~ 70 (299)
+..|.|...+- ..++.+.|..||.|||+|+.+.+.-..
T Consensus 71 ~~~I~v~~~ll----~~~~~~el~aVlaHElgH~~~~h~~~~ 108 (226)
T PF01435_consen 71 RKRIVVTSGLL----ESLSEDELAAVLAHELGHIKHRHILKS 108 (226)
T ss_dssp --EEEEEHHHH----HHSSHHHHHHHHHHHHHHHHTTHCCCC
T ss_pred CcEEEEeChhh----hcccHHHHHHHHHHHHHHHHcCCcchH
Confidence 34577776653 348889999999999999998877666
No 44
>PRK05457 heat shock protein HtpX; Provisional
Probab=83.05 E-value=0.77 Score=43.64 Aligned_cols=21 Identities=19% Similarity=0.420 Sum_probs=19.4
Q ss_pred CCHHHHHHHHHHHhhhcCCCC
Q 022290 46 FPYEQILDTMLHELCHNEYGP 66 (299)
Q Consensus 46 ~p~~~i~~v~lHELaH~~~~~ 66 (299)
++.++|..|+.|||.|+.+++
T Consensus 129 L~~~El~aVlAHElgHi~~~d 149 (284)
T PRK05457 129 MSRDEVEAVLAHEISHIANGD 149 (284)
T ss_pred CCHHHHHHHHHHHHHHHHcCC
Confidence 688999999999999999875
No 45
>PRK03001 M48 family peptidase; Provisional
Probab=83.00 E-value=0.81 Score=43.17 Aligned_cols=41 Identities=22% Similarity=0.145 Sum_probs=27.6
Q ss_pred ccceecCCCcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCC
Q 022290 21 LLGINIGGGAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGP 66 (299)
Q Consensus 21 llGlN~n~G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~ 66 (299)
.+|.+.+++ .|.|.--+- .-+..++|..||.|||+|+.|++
T Consensus 99 a~G~~~~~~-~Ivvt~gLl----~~l~~~El~aVlAHElgHi~~~h 139 (283)
T PRK03001 99 ATGRNPEHA-AVAATTGIL----RVLSEREIRGVMAHELAHVKHRD 139 (283)
T ss_pred EecCCCCCe-EEEecHHHH----hhCCHHHHHHHHHHHHHHHhCCC
Confidence 345554444 355544332 12578999999999999999874
No 46
>PRK02391 heat shock protein HtpX; Provisional
Probab=82.59 E-value=0.82 Score=43.73 Aligned_cols=22 Identities=18% Similarity=0.249 Sum_probs=19.7
Q ss_pred CCCHHHHHHHHHHHhhhcCCCC
Q 022290 45 FFPYEQILDTMLHELCHNEYGP 66 (299)
Q Consensus 45 f~p~~~i~~v~lHELaH~~~~~ 66 (299)
.+..++++.||.|||+|+.+++
T Consensus 127 ~L~~~El~aVlaHElgHi~~~d 148 (296)
T PRK02391 127 RLDPDELEAVLAHELSHVKNRD 148 (296)
T ss_pred hCCHHHHHHHHHHHHHHHHcCC
Confidence 3678999999999999999886
No 47
>PRK01345 heat shock protein HtpX; Provisional
Probab=82.49 E-value=0.82 Score=44.14 Aligned_cols=41 Identities=22% Similarity=0.174 Sum_probs=27.3
Q ss_pred ccceecCCCcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCC
Q 022290 21 LLGINIGGGAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGP 66 (299)
Q Consensus 21 llGlN~n~G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~ 66 (299)
.+|.+.+++ .|.+..-+- ..++.++|..||.|||.|+++++
T Consensus 99 a~G~~~~~~-~V~vt~gLL----~~L~~dEL~aVlAHElgHi~~~d 139 (317)
T PRK01345 99 ATGRNPENA-AVAATTGLL----QRLSPEEVAGVMAHELAHVKNRD 139 (317)
T ss_pred EecCCCCCe-EEEechHHH----hhCCHHHHHHHHHHHHHHHHcCC
Confidence 344443333 466653332 23578999999999999999755
No 48
>PRK01265 heat shock protein HtpX; Provisional
Probab=81.29 E-value=0.96 Score=44.02 Aligned_cols=42 Identities=21% Similarity=0.234 Sum_probs=28.9
Q ss_pred ccceecCCCcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCCC
Q 022290 21 LLGINIGGGAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGPH 67 (299)
Q Consensus 21 llGlN~n~G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~H 67 (299)
..|.+... ..|.|.--+- ..++.+.|..||.|||.|+.|++=
T Consensus 115 a~G~~~~~-~~Ivvt~gLl----~~l~~~El~aVlAHElgHik~~d~ 156 (324)
T PRK01265 115 AYGSPIAG-KRIAITLPLL----KILNRDEIKAVAGHELGHLKHRDV 156 (324)
T ss_pred EeccCCCC-CEEEEehHHH----hhCCHHHHHHHHHHHHHHHHcccH
Confidence 34444333 4576665543 336889999999999999987653
No 49
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=80.59 E-value=0.98 Score=27.19 Aligned_cols=22 Identities=32% Similarity=0.554 Sum_probs=19.6
Q ss_pred cCCccccccccCCccccccCCC
Q 022290 228 QCNMCTLLNQPLALTCEACGTQ 249 (299)
Q Consensus 228 ~C~~CT~~N~~~a~~C~aCgt~ 249 (299)
.|+.|.-.|+..+..|..||++
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCcCcchhhhCCc
Confidence 3899999999999999999975
No 50
>KOG3854 consensus SPRT-like metalloprotease [Function unknown]
Probab=80.58 E-value=1.1 Score=45.54 Aligned_cols=42 Identities=29% Similarity=0.389 Sum_probs=29.7
Q ss_pred CcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhc-------CCCCCChhHHHHHH
Q 022290 29 GAEVKLRLRRPNREWDFFPYEQILDTMLHELCHN-------EYGPHNADFYKLWD 76 (299)
Q Consensus 29 G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~-------~~~~H~~~F~~l~~ 76 (299)
-.+|.|-+.- .---+.|..||+|||||. .+..|.+.|-..-.
T Consensus 335 ~A~IeLs~kV------~tTAERir~TLiHEmCHaAaWv~dr~e~gHGd~wKrWa~ 383 (505)
T KOG3854|consen 335 YAKIELSDKV------CTTAERIRDTLIHEMCHAAAWVFDREELGHGDNWKRWAY 383 (505)
T ss_pred eeEEEehhhh------hhHHHHHHHHHHHHHHHHHHhhccccccCcchHHHHHHH
Confidence 3456665543 355688999999999995 27889988654433
No 51
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=80.10 E-value=1.1 Score=32.12 Aligned_cols=9 Identities=33% Similarity=1.302 Sum_probs=4.3
Q ss_pred CCcccCCcc
Q 022290 258 KGWSCKFCT 266 (299)
Q Consensus 258 ~~W~C~~Ct 266 (299)
..|.|+.|.
T Consensus 33 ~~w~CP~C~ 41 (50)
T cd00730 33 DDWVCPVCG 41 (50)
T ss_pred CCCCCCCCC
Confidence 345555543
No 52
>COG5100 NPL4 Nuclear pore protein [Nuclear structure]
Probab=79.58 E-value=0.47 Score=47.53 Aligned_cols=25 Identities=40% Similarity=0.844 Sum_probs=22.9
Q ss_pred CcccCCcccccCCCCccccccCCCC
Q 022290 259 GWSCKFCTLDNSSLSERCLACGEWR 283 (299)
Q Consensus 259 ~W~C~~Ct~~N~~~~~~C~~Cg~~r 283 (299)
.|.|+.|||.|+..|-+|+||.+.+
T Consensus 546 ~we~~~~~~i~~~~~~t~~m~~~~~ 570 (571)
T COG5100 546 RWECKMCTFINEKNSCTCEMCNSTR 570 (571)
T ss_pred HHHHHHHHHhcccCceEEEeecccC
Confidence 4999999999999999999998765
No 53
>cd04271 ZnMc_ADAM_fungal Zinc-dependent metalloprotease, ADAM_fungal subgroup. The adamalysin_like or ADAM (A Disintegrin And Metalloprotease) family of metalloproteases are integral membrane proteases acting on a variety of extracellular targets. They are involved in shedding soluble peptides or proteins from the cell surface. This subfamily contains fungal ADAMs, whose precise function has yet to be determined.
Probab=78.75 E-value=0.8 Score=42.13 Aligned_cols=18 Identities=22% Similarity=0.329 Sum_probs=16.6
Q ss_pred HHHHHHhhhcCCCCCChh
Q 022290 53 DTMLHELCHNEYGPHNAD 70 (299)
Q Consensus 53 ~v~lHELaH~~~~~H~~~ 70 (299)
.||+|||.|++-++||..
T Consensus 147 ~t~AHElGHnLGm~HD~~ 164 (228)
T cd04271 147 QVFAHEIGHTFGAVHDCT 164 (228)
T ss_pred eehhhhhhhhcCCCCCCC
Confidence 699999999999999964
No 54
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=78.23 E-value=1.1 Score=39.75 Aligned_cols=10 Identities=30% Similarity=1.185 Sum_probs=7.7
Q ss_pred CccCCccccc
Q 022290 226 MWQCNMCTLL 235 (299)
Q Consensus 226 ~W~C~~CT~~ 235 (299)
.|.|+.|.|+
T Consensus 134 ~~vC~vCGy~ 143 (166)
T COG1592 134 VWVCPVCGYT 143 (166)
T ss_pred EEEcCCCCCc
Confidence 6888888765
No 55
>PF01447 Peptidase_M4: Thermolysin metallopeptidase, catalytic domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification. ; InterPro: IPR013856 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases that belong to the MEROPS peptidase family M4 (thermolysin family, clan MA(E)). The protein fold of the peptidase domain of thermolysin, is the type example for members of the clan MA. The thermolysin family is composed only of secreted eubacterial endopeptidases. The zinc-binding residues are H-142, H-146 and E-166, with E-143 acting as the catalytic residue. Thermolysin also contains 4 calcium-binding sites, which contribute to its unusual thermostability. The family also includes enzymes from a number of pathogens, including Legionella and Listeria, and the protein pseudolysin, all with a substrate specificity for an aromatic residue in the P1' position. Three-dimensional structure analysis has shown that the enzymes undergo a hinge-bend motion during catalysis. Pseudolysin has a broader specificity, acting on large molecules such as elastin and collagen, possibly due to its wider active site cleft []. This entry represents a domain found in peptidase M4 family members.; GO: 0004222 metalloendopeptidase activity; PDB: 3NQX_A 3NQZ_B 3NQY_B 1BQB_A 1U4G_A 1EZM_A 3DBK_A 1ESP_A 1NPC_A 1LND_E ....
Probab=77.54 E-value=1.5 Score=38.12 Aligned_cols=21 Identities=38% Similarity=0.556 Sum_probs=16.5
Q ss_pred CCCCCHHHHHHHHHHHhhhcC
Q 022290 43 WDFFPYEQILDTMLHELCHNE 63 (299)
Q Consensus 43 ~~f~p~~~i~~v~lHELaH~~ 63 (299)
..|.|+-.-++|+.|||+|-|
T Consensus 127 ~~f~~~~~~lDVvaHEltHGV 147 (150)
T PF01447_consen 127 QIFKPFASSLDVVAHELTHGV 147 (150)
T ss_dssp SSBS-GGG-HHHHHHHHHHHH
T ss_pred cccccCccccceeeecccccc
Confidence 378999998899999999964
No 56
>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]
Probab=77.47 E-value=1.2 Score=43.74 Aligned_cols=61 Identities=13% Similarity=0.214 Sum_probs=48.0
Q ss_pred CCCCccCC--ccccccccCCccccccCCCCCCCC-------------------CCCCCcccCCcccccCCCCccccccCC
Q 022290 223 VGQMWQCN--MCTLLNQPLALTCEACGTQRNKSV-------------------GNLKGWSCKFCTLDNSSLSERCLACGE 281 (299)
Q Consensus 223 ~~~~W~C~--~CT~~N~~~a~~C~aCgt~rp~~~-------------------~~~~~W~C~~Ct~~N~~~~~~C~~Cg~ 281 (299)
..-.|.|+ +|.-.|...+++|..|...++... .....|.|+.|+.+|+.....|- .+
T Consensus 68 ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~g--n~ 145 (351)
T KOG1995|consen 68 TIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCG--NT 145 (351)
T ss_pred cceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccC--CC
Confidence 34579997 899999999999999998887632 23457999999999998888887 55
Q ss_pred CCCC
Q 022290 282 WRYS 285 (299)
Q Consensus 282 ~r~~ 285 (299)
++.+
T Consensus 146 ikvs 149 (351)
T KOG1995|consen 146 IKVS 149 (351)
T ss_pred chhh
Confidence 5544
No 57
>PF10026 DUF2268: Predicted Zn-dependent protease (DUF2268); InterPro: IPR018728 This domain, found in various hypothetical bacterial proteins, as well as predicted zinc dependent proteases, has no known function.
Probab=77.30 E-value=2.8 Score=37.49 Aligned_cols=47 Identities=26% Similarity=0.236 Sum_probs=31.6
Q ss_pred cEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCCCCh---hHHHHHHHHHHH
Q 022290 30 AEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGPHNA---DFYKLWDEIRKE 81 (299)
Q Consensus 30 ~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~H~~---~F~~l~~~l~~e 81 (299)
.+|.|-| .+. -...+.|..+|+||+-|++...+-. .=..|++.+.-|
T Consensus 49 ~~i~l~~-~~~----~~~~~~l~~~iaHE~hH~~r~~~~~~~~~~~TLld~~I~E 98 (195)
T PF10026_consen 49 GYIFLFL-LPN----DYSLEELPALIAHEYHHNCRYEQIGWDPEDTTLLDSLIME 98 (195)
T ss_pred CEEEEEe-cCC----cccHHHHHHHHHHHHHHHHHHhccCCCCCCCCHHHHHHHh
Confidence 4687776 432 2556799999999999998654332 334566666554
No 58
>COG4900 Predicted metallopeptidase [General function prediction only]
Probab=77.02 E-value=3.9 Score=34.35 Aligned_cols=47 Identities=15% Similarity=0.329 Sum_probs=32.0
Q ss_pred cCCCcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCC------CCCC--hhHHHHHH
Q 022290 26 IGGGAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEY------GPHN--ADFYKLWD 76 (299)
Q Consensus 26 ~n~G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~------~~H~--~~F~~l~~ 76 (299)
.|.+-.|.|--.. .--+|-+.-..||+|||.|+-. ..|+ .+||....
T Consensus 59 lnP~YviEl~sek----F~rLs~~ekvKviiHEllHIP~tfSGgLRaHg~~vn~rrv~k 113 (133)
T COG4900 59 LNPVYVIELLSEK----FKRLSCAEKVKVIIHELLHIPATFSGGLRAHGPLVNFRRVYK 113 (133)
T ss_pred CCCeeeeeeehhh----cCCCChHHHHHHHHHHHhcCcccccCccccCCcchhHHHHHH
Confidence 4556556553221 1237788888999999999975 3788 78887554
No 59
>COG5100 NPL4 Nuclear pore protein [Nuclear structure]
Probab=76.03 E-value=0.65 Score=46.57 Aligned_cols=25 Identities=44% Similarity=1.147 Sum_probs=23.1
Q ss_pred CccCCccccccccCCccccccCCCC
Q 022290 226 MWQCNMCTLLNQPLALTCEACGTQR 250 (299)
Q Consensus 226 ~W~C~~CT~~N~~~a~~C~aCgt~r 250 (299)
.|.|..|||+|.....+|+||...+
T Consensus 546 ~we~~~~~~i~~~~~~t~~m~~~~~ 570 (571)
T COG5100 546 RWECKMCTFINEKNSCTCEMCNSTR 570 (571)
T ss_pred HHHHHHHHHhcccCceEEEeecccC
Confidence 4999999999999999999998765
No 60
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=73.96 E-value=2.2 Score=33.09 Aligned_cols=32 Identities=19% Similarity=0.136 Sum_probs=18.7
Q ss_pred CcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCC
Q 022290 29 GAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYG 65 (299)
Q Consensus 29 G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~ 65 (299)
|+.|.|+--... .....=..+|.|||+|.+.-
T Consensus 44 G~~I~f~~g~~~-----~~s~~~~~llaHEl~Hv~Qq 75 (79)
T PF13699_consen 44 GNDIYFAPGKYN-----PDSPEGRALLAHELAHVVQQ 75 (79)
T ss_pred CCEEEEcCCCcC-----CCCCCcchhHhHHHHHHHhh
Confidence 888988432100 00011247899999998753
No 61
>cd04272 ZnMc_salivary_gland_MPs Zinc-dependent metalloprotease, salivary_gland_MPs. Metalloproteases secreted by the salivary glands of arthropods.
Probab=72.95 E-value=2 Score=38.78 Aligned_cols=19 Identities=42% Similarity=0.564 Sum_probs=17.6
Q ss_pred HHHHHHHhhhcCCCCCChh
Q 022290 52 LDTMLHELCHNEYGPHNAD 70 (299)
Q Consensus 52 ~~v~lHELaH~~~~~H~~~ 70 (299)
..||+|||.|++-++||..
T Consensus 146 ~~~~AHElGH~lG~~HD~~ 164 (220)
T cd04272 146 VYTMTHELAHLLGAPHDGS 164 (220)
T ss_pred HHHHHHHHHHHhCCCCCCC
Confidence 6999999999999999975
No 62
>PF13582 Reprolysin_3: Metallo-peptidase family M12B Reprolysin-like; PDB: 3P24_C.
Probab=72.12 E-value=1.6 Score=35.25 Aligned_cols=16 Identities=44% Similarity=0.499 Sum_probs=11.8
Q ss_pred HHHHHHhhhcCCCCCC
Q 022290 53 DTMLHELCHNEYGPHN 68 (299)
Q Consensus 53 ~v~lHELaH~~~~~H~ 68 (299)
+|+.|||-|+.-.+||
T Consensus 109 ~~~~HEiGH~lGl~Hd 124 (124)
T PF13582_consen 109 DTFAHEIGHNLGLNHD 124 (124)
T ss_dssp THHHHHHHHHTT----
T ss_pred eEeeehhhHhcCCCCC
Confidence 9999999999999996
No 63
>cd04267 ZnMc_ADAM_like Zinc-dependent metalloprotease, ADAM_like or reprolysin_like subgroup. The adamalysin_like or ADAM family of metalloproteases contains proteolytic domains from snake venoms, proteases from the mammalian reproductive tract, and the tumor necrosis factor alpha convertase, TACE. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions.
Probab=71.26 E-value=2.1 Score=37.43 Aligned_cols=22 Identities=36% Similarity=0.287 Sum_probs=19.1
Q ss_pred HHHHHHHHHHhhhcCCCCCChh
Q 022290 49 EQILDTMLHELCHNEYGPHNAD 70 (299)
Q Consensus 49 ~~i~~v~lHELaH~~~~~H~~~ 70 (299)
.....||+|||.|++-..||..
T Consensus 131 ~~~~~~~aHElGH~lG~~HD~~ 152 (192)
T cd04267 131 LLTALTMAHELGHNLGAEHDGG 152 (192)
T ss_pred eeehhhhhhhHHhhcCCcCCCC
Confidence 3456799999999999999976
No 64
>PF14521 Aspzincin_M35: Lysine-specific metallo-endopeptidase ; PDB: 2X3C_A 2X3A_A 2X3B_A 1GE7_B 1GE6_A 1GE5_A 1G12_A.
Probab=70.13 E-value=3.4 Score=35.47 Aligned_cols=23 Identities=22% Similarity=0.284 Sum_probs=14.4
Q ss_pred HHHHHHHHHHhhhcCCCCCChhH
Q 022290 49 EQILDTMLHELCHNEYGPHNADF 71 (299)
Q Consensus 49 ~~i~~v~lHELaH~~~~~H~~~F 71 (299)
..-+.||+|||+|+.-.-+..++
T Consensus 94 ~Sk~~TLiHE~SHf~~~~~T~D~ 116 (148)
T PF14521_consen 94 DSKEGTLIHEWSHFTAVGGTDDY 116 (148)
T ss_dssp T-HHHHHHHHHHHSCCCT--B-S
T ss_pred CchHHHHHHhhhhhhhhcCCCcc
Confidence 44679999999997654444444
No 65
>PF13688 Reprolysin_5: Metallo-peptidase family M12; PDB: 2FV5_B 3EWJ_A 3KME_A 3L0T_B 1BKC_E 3G42_D 2I47_D 2FV9_B 3LEA_A 1ZXC_B ....
Probab=69.79 E-value=3.1 Score=36.40 Aligned_cols=25 Identities=36% Similarity=0.377 Sum_probs=16.4
Q ss_pred CCHHHHHHHHHHHhhhcCCCCCChh
Q 022290 46 FPYEQILDTMLHELCHNEYGPHNAD 70 (299)
Q Consensus 46 ~p~~~i~~v~lHELaH~~~~~H~~~ 70 (299)
.+...-..|++|||.|+.-.+||..
T Consensus 137 ~~~~~~~~~~AHEiGH~lGa~HD~~ 161 (196)
T PF13688_consen 137 PPTYNGAITFAHEIGHNLGAPHDGD 161 (196)
T ss_dssp --HHHHHHHHHHHHHHHTT-----S
T ss_pred CCCCceehhhHHhHHHhcCCCCCCC
Confidence 5677888999999999999999865
No 66
>cd04269 ZnMc_adamalysin_II_like Zinc-dependent metalloprotease; adamalysin_II_like subfamily. Adamalysin II is a snake venom zinc endopeptidase. This subfamily contains other snake venom metalloproteinases, as well as membrane-anchored metalloproteases belonging to the ADAM family. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions.
Probab=69.77 E-value=3.5 Score=36.14 Aligned_cols=23 Identities=35% Similarity=0.244 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHhhhcCCCCCChh
Q 022290 48 YEQILDTMLHELCHNEYGPHNAD 70 (299)
Q Consensus 48 ~~~i~~v~lHELaH~~~~~H~~~ 70 (299)
+.....||+|||.|+.-.+||..
T Consensus 128 ~~~~a~~~AHElGH~lG~~HD~~ 150 (194)
T cd04269 128 LLLFAVTMAHELGHNLGMEHDDG 150 (194)
T ss_pred hHHHHHHHHHHHHhhcCCCcCCC
Confidence 34557899999999999999987
No 67
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=69.00 E-value=2.6 Score=30.57 Aligned_cols=35 Identities=20% Similarity=0.392 Sum_probs=20.5
Q ss_pred ccccCCccccccCCCCCCC---CCCCCCcccCCccccc
Q 022290 235 LNQPLALTCEACGTQRNKS---VGNLKGWSCKFCTLDN 269 (299)
Q Consensus 235 ~N~~~a~~C~aCgt~rp~~---~~~~~~W~C~~Ct~~N 269 (299)
.+...++.|..|..-.... ....-.|.|..|.+.|
T Consensus 17 ~~~r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~N 54 (54)
T PF10058_consen 17 PSNRYALICSKCFSHNGLAPKEEFEEIQYRCPYCGALN 54 (54)
T ss_pred ccCceeEECcccchhhcccccccCCceEEEcCCCCCcC
Confidence 3444455566665433221 1334479999999887
No 68
>PF13574 Reprolysin_2: Metallo-peptidase family M12B Reprolysin-like; PDB: 1KAP_P 1JIW_P 1AKL_A 1OM7_A 1OM8_A 1O0T_A 1OM6_A 1H71_P 1O0Q_A 1OMJ_A ....
Probab=68.23 E-value=2.3 Score=37.21 Aligned_cols=20 Identities=45% Similarity=0.602 Sum_probs=15.2
Q ss_pred HHHHHHHHhhhcCCCCCChh
Q 022290 51 ILDTMLHELCHNEYGPHNAD 70 (299)
Q Consensus 51 i~~v~lHELaH~~~~~H~~~ 70 (299)
-.+|++|||.|+.-.+|+-.
T Consensus 111 ~~~~~aHElGH~lGa~Hd~~ 130 (173)
T PF13574_consen 111 GIDTFAHELGHQLGAPHDFD 130 (173)
T ss_dssp HHHHHHHHHHHHHT---SSS
T ss_pred eeeeehhhhHhhcCCCCCCC
Confidence 55779999999999999988
No 69
>PF12773 DZR: Double zinc ribbon
Probab=66.67 E-value=4.4 Score=27.97 Aligned_cols=25 Identities=32% Similarity=0.526 Sum_probs=21.2
Q ss_pred CCCCccCCccccccccCCccccccC
Q 022290 223 VGQMWQCNMCTLLNQPLALTCEACG 247 (299)
Q Consensus 223 ~~~~W~C~~CT~~N~~~a~~C~aCg 247 (299)
....+.|+.|...|...+..|..||
T Consensus 26 ~~~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 26 DQSKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred cCCCCCCcCCcCCCcCCcCccCccc
Confidence 3457899999999999999999886
No 70
>PF09768 Peptidase_M76: Peptidase M76 family; InterPro: IPR019165 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. Mitochondrial inner membrane protease ATP23 has two roles in the assembly of mitochondrial ATPase. Firstly, it acts as a protease that removes the N-terminal 10 residues of mitochondrial ATPase CF(0) subunit 6 (ATP6) at the intermembrane space side. Secondly, it is involved in the correct assembly of the membrane-embedded ATPase CF(0) particle, probably mediating association of ATP6 with the subunit 9 ring [, ].; GO: 0004222 metalloendopeptidase activity
Probab=65.52 E-value=5 Score=35.76 Aligned_cols=19 Identities=32% Similarity=0.371 Sum_probs=16.3
Q ss_pred CCCHHHHHHHHHHHhhhcC
Q 022290 45 FFPYEQILDTMLHELCHNE 63 (299)
Q Consensus 45 f~p~~~i~~v~lHELaH~~ 63 (299)
+.....++.||.|||.|..
T Consensus 65 ~~~~~~l~~~l~HELIHay 83 (173)
T PF09768_consen 65 IRSQGHLEDTLTHELIHAY 83 (173)
T ss_pred CCCHHHHHHHHHHHHHHHH
Confidence 4667899999999999974
No 71
>PRK15410 DgsA anti-repressor MtfA; Provisional
Probab=65.38 E-value=5.9 Score=37.56 Aligned_cols=62 Identities=13% Similarity=0.139 Sum_probs=39.6
Q ss_pred CccceecCCCcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCCCCh----------hHHHHHHHHH-HHHHHHH
Q 022290 20 SLLGINIGGGAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGPHNA----------DFYKLWDEIR-KECDELM 86 (299)
Q Consensus 20 ~llGlN~n~G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~H~~----------~F~~l~~~l~-~e~~~l~ 86 (299)
.++|-....| .|.|.+..-.. .+.+ + =..|++||+||.+.+.++. ..+..|.+++ .+|+.|.
T Consensus 116 ~~~GEaw~~G-pVVLSW~d~~~--~~~~-d-g~NVvIHEFAH~LDm~~G~~adG~PpL~~~~~~~W~~~~~~~~~~l~ 188 (260)
T PRK15410 116 VQSGQSWQQG-PIVLNWLDIQD--SFDA-S-GFNLIIHEVAHKLDMRNGDRASGVPFIPLREVAGWEHDLHAAMNNIQ 188 (260)
T ss_pred cccccCcCCC-cEEEEHHHhhc--ccCC-C-CcchhHhHHHhHhhhhcCCCCCCCCCCCchhHHHHHHHHHHHHHHHH
Confidence 4667777777 58888876321 2322 2 3589999999999988744 3445555444 4555554
No 72
>PF01421 Reprolysin: Reprolysin (M12B) family zinc metalloprotease This Prosite motif covers only the active site.; InterPro: IPR001590 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M12, subfamily M12B (adamalysin family, clan (MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH []. The adamalysins are zinc dependent endopeptidases found in snake venom. There are some mammalian proteins such as P78325 from SWISSPROT, and fertilin Q28472 from SWISSPROT. Fertilin and closely related proteins appear to not have some active site residues and may not be active enzymes. CD156 (also called ADAM8 (3.4.24 from EC) or MS2 human) has been implicated in extravasation of leukocytes. CD molecules are leucocyte antigens on cell surfaces. CD antigens nomenclature is updated at Protein Reviews On The Web (http://prow.nci.nih.gov/). ; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2E3X_A 2W15_A 2W14_A 2W13_A 2W12_A 1ND1_A 3K7L_A 2DW2_A 2DW0_B 2DW1_A ....
Probab=65.00 E-value=4.8 Score=35.46 Aligned_cols=25 Identities=32% Similarity=0.272 Sum_probs=18.8
Q ss_pred CCHHHHHHHHHHHhhhcCCCCCChh
Q 022290 46 FPYEQILDTMLHELCHNEYGPHNAD 70 (299)
Q Consensus 46 ~p~~~i~~v~lHELaH~~~~~H~~~ 70 (299)
..+...-.+|+|||.|+.-++||..
T Consensus 126 ~~~~~~a~~~AHelGH~lGm~HD~~ 150 (199)
T PF01421_consen 126 RSGLSFAVIIAHELGHNLGMPHDGD 150 (199)
T ss_dssp SSHHHHHHHHHHHHHHHTT---TTT
T ss_pred chhHHHHHHHHHHHHHhcCCCCCCC
Confidence 4456777999999999999999987
No 73
>PF06262 DUF1025: Possibl zinc metallo-peptidase; InterPro: IPR010428 This is a family of bacterial protein with undetermined function.; PDB: 3E11_A.
Probab=64.54 E-value=4.4 Score=32.81 Aligned_cols=16 Identities=44% Similarity=0.580 Sum_probs=13.7
Q ss_pred HHHHHHHHHHhhhcCC
Q 022290 49 EQILDTMLHELCHNEY 64 (299)
Q Consensus 49 ~~i~~v~lHELaH~~~ 64 (299)
+.|..|++||++|..-
T Consensus 71 ~~I~~tlvhEiah~fG 86 (97)
T PF06262_consen 71 ELIRDTLVHEIAHHFG 86 (97)
T ss_dssp HHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHcC
Confidence 5688999999999764
No 74
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=64.43 E-value=2.7 Score=29.72 Aligned_cols=10 Identities=30% Similarity=1.096 Sum_probs=3.9
Q ss_pred CCCcccCCcc
Q 022290 257 LKGWSCKFCT 266 (299)
Q Consensus 257 ~~~W~C~~Ct 266 (299)
+..|.|+.|.
T Consensus 32 p~~w~CP~C~ 41 (47)
T PF00301_consen 32 PDDWVCPVCG 41 (47)
T ss_dssp -TT-B-TTTS
T ss_pred CCCCcCcCCC
Confidence 3456666554
No 75
>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]
Probab=64.27 E-value=6.3 Score=38.84 Aligned_cols=32 Identities=22% Similarity=0.533 Sum_probs=28.7
Q ss_pred CCCCCccCC-ccccccccCCccccccCCCCCCC
Q 022290 222 DVGQMWQCN-MCTLLNQPLALTCEACGTQRNKS 253 (299)
Q Consensus 222 ~~~~~W~C~-~CT~~N~~~a~~C~aCgt~rp~~ 253 (299)
..+..|.|+ .|..+|+.....|..|.++||..
T Consensus 214 ~~d~Dw~c~~~c~N~nfa~r~~cnrck~~Kp~~ 246 (351)
T KOG1995|consen 214 DEDGDWDCPPSCGNRNFAWREECNRCKAPKPER 246 (351)
T ss_pred cccccccccccccccccccccccccccCCCccc
Confidence 456789999 99999999999999999999854
No 76
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=62.84 E-value=5 Score=38.80 Aligned_cols=52 Identities=13% Similarity=0.069 Sum_probs=33.7
Q ss_pred EEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCCCChhHHHHH-HHHHHHHHHHHHcccc
Q 022290 33 KLRLRRPNREWDFFPYEQILDTMLHELCHNEYGPHNADFYKLW-DEIRKECDELMAKGIT 91 (299)
Q Consensus 33 ~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~H~~~F~~l~-~~l~~e~~~l~~~G~~ 91 (299)
.|+||.. .-+.+...++.+ +..-+-++.|.-|-+-+ .+|.+++..++++-++
T Consensus 125 ~l~lRa~----Gtys~kvtDpi~---fi~~I~g~~dvy~v~di~~q~ls~~m~al~tai~ 177 (345)
T COG4260 125 ELFLRAH----GTYSIKVTDPIL---FIQQIPGNRDVYTVDDINQQYLSEFMGALATAIN 177 (345)
T ss_pred eeEEeec----ceEEEEecCHHH---HHHhccCCCceEEHHHHHHHHHHHHHHHHHHHHH
Confidence 4666663 345566666665 56667777777776544 4677888877776544
No 77
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=62.12 E-value=11 Score=39.03 Aligned_cols=62 Identities=21% Similarity=0.461 Sum_probs=41.7
Q ss_pred CCCCCCCCc-cCCccccccccCC---ccccccCCCCCCC---------------CCCCCCcccCCcccccCCCCcccccc
Q 022290 219 KAVDVGQMW-QCNMCTLLNQPLA---LTCEACGTQRNKS---------------VGNLKGWSCKFCTLDNSSLSERCLAC 279 (299)
Q Consensus 219 ~~~~~~~~W-~C~~CT~~N~~~a---~~C~aCgt~rp~~---------------~~~~~~W~C~~Ct~~N~~~~~~C~~C 279 (299)
+.+....+| .|-+|.-.|...+ +.|..||..-... .-....|.|..|.+--.. ..|+.|
T Consensus 111 ~~~Sapkk~~iCcVClg~rs~da~ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~Gvs~--P~CElC 188 (707)
T KOG0957|consen 111 RTPSAPKKAVICCVCLGQRSVDAGEILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLYGVSL--PHCELC 188 (707)
T ss_pred cccCccccceEEEEeecCccccccceeeccccCceecccccccccccccCCCCccCCCCchhhhhHhcCCCC--CccccC
Confidence 344555789 9999988885543 6799998653211 023467999999885443 678888
Q ss_pred CCC
Q 022290 280 GEW 282 (299)
Q Consensus 280 g~~ 282 (299)
-..
T Consensus 189 Pn~ 191 (707)
T KOG0957|consen 189 PNR 191 (707)
T ss_pred CCc
Confidence 543
No 78
>PF02102 Peptidase_M35: Deuterolysin metalloprotease (M35) family; InterPro: IPR001384 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M35 (deuterolysin family, clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. Deuterolysin is a microbial zinc-containing metalloprotease that shows some similarity to thermolysin []. The protein is expressed with a possible 19-residue signal sequence, a 155-residue propeptide, and an active peptide of 177 residues []. The latter contains an HEXXH motif towards the C terminus, but the other zinc ligands are as yet undetermined [, ].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 1EB6_A.
Probab=61.76 E-value=4.3 Score=40.18 Aligned_cols=21 Identities=38% Similarity=0.637 Sum_probs=12.7
Q ss_pred HHHHHHHHHhhhcC--CCCCChh
Q 022290 50 QILDTMLHELCHNE--YGPHNAD 70 (299)
Q Consensus 50 ~i~~v~lHELaH~~--~~~H~~~ 70 (299)
.-..|+||||+|+. +.++-.+
T Consensus 296 Dqatt~LHE~TH~~~V~~pgt~D 318 (359)
T PF02102_consen 296 DQATTTLHEMTHAPAVYSPGTDD 318 (359)
T ss_dssp -HHHHHHHHHHT-TTTSSS--B-
T ss_pred CccchhhhhhhccccccCCCccc
Confidence 45689999999995 5555543
No 79
>COG0308 PepN Aminopeptidase N [Amino acid transport and metabolism]
Probab=61.45 E-value=5.2 Score=43.70 Aligned_cols=22 Identities=32% Similarity=0.581 Sum_probs=18.6
Q ss_pred CCHHHHHHHHHHHhhhcCCCCC
Q 022290 46 FPYEQILDTMLHELCHNEYGPH 67 (299)
Q Consensus 46 ~p~~~i~~v~lHELaH~~~~~H 67 (299)
..++.|..|++|||+|+..||=
T Consensus 302 ~~~~~~~~viaHElaHqWfGnl 323 (859)
T COG0308 302 SDYENVEEVIAHELAHQWFGNL 323 (859)
T ss_pred HHHHHHHHHHHHHHhhhcccce
Confidence 4457888899999999999974
No 80
>PF00413 Peptidase_M10: Matrixin This Prosite motif covers only the active site.; InterPro: IPR001818 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M10 (clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. Sequences having this domain are extracellular metalloproteases, such as collagenase and stromelysin, which degrade the extracellular matrix, are known as matrixins. They are zinc-dependent, calcium-activated proteases synthesised as inactive precursors (zymogens), which are proteolytically cleaved to yield the active enzyme [, ]. All matrixins and related proteins possess 2 domains: an N-terminal domain, and a zinc-binding active site domain. The N-terminal domain peptide, cleaved during the activation step, includes a conserved PRCGVPDV octapeptide, known as the cysteine switch, whose Cys residue chelates the active site zinc atom, rendering the enzyme inactive [, ]. The active enzyme degrades components of the extracellular matrix, playing a role in the initial steps of tissue remodelling during morphogenesis, wound healing, angiogenesis and tumour invasion [, ].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis, 0031012 extracellular matrix; PDB: 1Q3A_C 3V96_B 1HV5_D 1CXV_A 1SRP_A 1FBL_A 1ZVX_A 1JH1_A 1I76_A 2OY4_A ....
Probab=61.23 E-value=4.5 Score=33.64 Aligned_cols=24 Identities=17% Similarity=0.117 Sum_probs=20.2
Q ss_pred CCHHHHHHHHHHHhhhcCCCCCCh
Q 022290 46 FPYEQILDTMLHELCHNEYGPHNA 69 (299)
Q Consensus 46 ~p~~~i~~v~lHELaH~~~~~H~~ 69 (299)
.+...+..|++|||-|.+--.|+.
T Consensus 100 ~~~~~~~~v~~HEiGHaLGL~H~~ 123 (154)
T PF00413_consen 100 DSGNDLQSVAIHEIGHALGLDHSN 123 (154)
T ss_dssp SSSEEHHHHHHHHHHHHTTBESSS
T ss_pred hhhhhhhhhhhhccccccCcCcCC
Confidence 455678899999999999999974
No 81
>cd04273 ZnMc_ADAMTS_like Zinc-dependent metalloprotease, ADAMTS_like subgroup. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions. This particular subfamily represents domain architectures that combine ADAM-like metalloproteinases with thrombospondin type-1 repeats. ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) proteinases are inhibited by TIMPs (tissue inhibitors of metalloproteinases), and they play roles in coagulation, angiogenesis, development and progression of arthritis. They hydrolyze the von Willebrand factor precursor and various components of the extracellular matrix.
Probab=60.92 E-value=2.2 Score=38.19 Aligned_cols=20 Identities=40% Similarity=0.375 Sum_probs=18.0
Q ss_pred HHHHHHHHhhhcCCCCCChh
Q 022290 51 ILDTMLHELCHNEYGPHNAD 70 (299)
Q Consensus 51 i~~v~lHELaH~~~~~H~~~ 70 (299)
...||.|||.|+.-..||..
T Consensus 140 ~a~~~aHElGH~LG~~HD~~ 159 (207)
T cd04273 140 SAFTIAHELGHVLGMPHDGD 159 (207)
T ss_pred eEEeeeeechhhcCCCCCCC
Confidence 34899999999999999987
No 82
>PF06167 Peptidase_M90: Glucose-regulated metallo-peptidase M90; InterPro: IPR010384 MtfA (earlier known as YeeI) is a transcription factor that binds Mlc (make large colonies), itself a repressor of glucose and hence a protein important in regulation of the phosphoenolpyruvate:glucose-phosphotransferase (PtsG) system, the major glucose transporter in Escherichia coli. Mlc is a repressor of ptsG, and MtfA is found to bind and inactivate Mlc with high affinity []. The membrane-bound protein EIICBGlc encoded by the ptsG gene is the major glucose transporter in E. coli. ; PDB: 3DL1_A 3KHI_A.
Probab=60.87 E-value=8.1 Score=36.34 Aligned_cols=66 Identities=23% Similarity=0.284 Sum_probs=32.3
Q ss_pred CccceecCCCcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCC----------CCChhHHHHHHHHH-HHHHHHHHc
Q 022290 20 SLLGINIGGGAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYG----------PHNADFYKLWDEIR-KECDELMAK 88 (299)
Q Consensus 20 ~llGlN~n~G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~----------~H~~~F~~l~~~l~-~e~~~l~~~ 88 (299)
-++|-.+..| .|.|.+-.-. ..+.....=..|++||+||.+.+ -|....+.-|.+++ ++|+.|..+
T Consensus 126 ~~~Geaw~~G-~vvLSW~~~~--~g~~~~~dg~NVviHEfAH~LD~~~g~adG~P~l~~~~~~~~W~~~~~~~~~~l~~~ 202 (253)
T PF06167_consen 126 VLLGEAWERG-PVVLSWEDVQ--EGFENPNDGHNVVIHEFAHKLDMEDGAADGVPPLHPGMSYRRWHKVFSAEYERLRER 202 (253)
T ss_dssp T--------S--EEEEHHHHH--HCT--SSSS--HHHHHHHHHHHCTTS--SS--S---GGGHHHHHHHHHHHHHHHHHH
T ss_pred hhhhccccCC-cEEEEHHHHh--hccCCCCCCcchHHHHHHHHHHhhcCCCCCCCccCCcccHHHHHHHHHHHHHHHHHH
Confidence 3556666666 4777765421 12223333348999999999855 25666777776665 567777654
No 83
>PF12725 DUF3810: Protein of unknown function (DUF3810); InterPro: IPR024294 This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 333 and 377 amino acids in length and contain a conserved HEXXH sequence motif that is characteristic of metallopeptidases. This family may therefore belong to an as yet uncharacterised family of peptidase enzymes.
Probab=58.27 E-value=3 Score=40.36 Aligned_cols=46 Identities=22% Similarity=0.185 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHhhhcCC--CCCChhHHHHHHHHHHHHHHHHHcccc
Q 022290 46 FPYEQILDTMLHELCHNEY--GPHNADFYKLWDEIRKECDELMAKGIT 91 (299)
Q Consensus 46 ~p~~~i~~v~lHELaH~~~--~~H~~~F~~l~~~l~~e~~~l~~~G~~ 91 (299)
+|.-.+=.|++|||||..- ..=.++|++.|.-...+=..+...||.
T Consensus 191 ~p~~~~P~T~~HElAHq~G~a~E~EANFiayLac~~s~d~~frYSgy~ 238 (318)
T PF12725_consen 191 LPPYSLPFTICHELAHQLGFASEDEANFIAYLACINSPDPYFRYSGYL 238 (318)
T ss_pred CCcccccHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCChheeHHHHH
Confidence 3444455799999999983 355678999988766555555555543
No 84
>cd04278 ZnMc_MMP Zinc-dependent metalloprotease, matrix metalloproteinase (MMP) sub-family. MMPs are responsible for a great deal of pericellular proteolysis of extracellular matrix and cell surface molecules, playing crucial roles in morphogenesis, cell fate specification, cell migration, tissue repair, tumorigenesis, gain or loss of tissue-specific functions, and apoptosis. In many instances, they are anchored to cell membranes via trans-membrane domains, and their activity is controlled via TIMPs (tissue inhibitors of metalloproteinases).
Probab=57.53 E-value=11 Score=31.95 Aligned_cols=40 Identities=10% Similarity=-0.022 Sum_probs=26.1
Q ss_pred cEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCCCCh
Q 022290 30 AEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGPHNA 69 (299)
Q Consensus 30 ~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~H~~ 69 (299)
..|.|+......-..-.+...+..|++|||-|.+--.|+.
T Consensus 86 g~i~~~~~~~~~~~~~~~~~~~~~~~~HEiGHaLGL~H~~ 125 (157)
T cd04278 86 GDIHFDDDEQWTLGSDSGGTDLFSVAAHEIGHALGLGHSS 125 (157)
T ss_pred eeEEECCCcccccCCCCccchHHHHHHHHhccccccCCCC
Confidence 3577774332110000245679999999999999999985
No 85
>PF13203 DUF2201_N: Putative metallopeptidase domain
Probab=57.41 E-value=7.6 Score=36.44 Aligned_cols=57 Identities=18% Similarity=0.212 Sum_probs=38.6
Q ss_pred CcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCC----------CChhHHHHHHHHHHHHHHHHHccc
Q 022290 29 GAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGP----------HNADFYKLWDEIRKECDELMAKGI 90 (299)
Q Consensus 29 G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~----------H~~~F~~l~~~l~~e~~~l~~~G~ 90 (299)
|..|.++-..- .-++.+.+..+++||+-|++... .+...|++--.+.-+.. |...|+
T Consensus 42 g~~l~~nP~~~----~~l~~~~~~~~l~HevlH~~~~H~~r~~~~~~~~d~~~wn~A~Di~VN~~-L~~~~~ 108 (292)
T PF13203_consen 42 GRRLYYNPEFL----ESLSPEERVGLLLHEVLHCLLRHPWRRGGLRKRRDPELWNLACDIAVNQY-LDEAGF 108 (292)
T ss_pred CcEEEECcHHH----hcCCHHHHHHHHHHHHHHHHccchhhhccccccccHHHHHHHhHHHHHHH-HHHcCC
Confidence 44788887763 23577889999999999998653 56677777666554432 333344
No 86
>COG1773 Rubredoxin [Energy production and conversion]
Probab=57.26 E-value=5.6 Score=29.18 Aligned_cols=40 Identities=20% Similarity=0.607 Sum_probs=24.2
Q ss_pred CccCCcccccccc--CCccccccCCCCCCCCCCCCCcccCCccc
Q 022290 226 MWQCNMCTLLNQP--LALTCEACGTQRNKSVGNLKGWSCKFCTL 267 (299)
Q Consensus 226 ~W~C~~CT~~N~~--~a~~C~aCgt~rp~~~~~~~~W~C~~Ct~ 267 (299)
.|.|..|.++=.+ ....|..|...+-. .-+..|.|+.|++
T Consensus 3 ~~~C~~CG~vYd~e~Gdp~~gi~pgT~fe--dlPd~w~CP~Cg~ 44 (55)
T COG1773 3 RWRCSVCGYVYDPEKGDPRCGIAPGTPFE--DLPDDWVCPECGV 44 (55)
T ss_pred ceEecCCceEeccccCCccCCCCCCCchh--hCCCccCCCCCCC
Confidence 6888888887433 33456666544311 1245688887775
No 87
>TIGR02414 pepN_proteo aminopeptidase N, Escherichia coli type. The M1 family of zinc metallopeptidases contains a number of distinct, well-separated clades of proteins with aminopeptidase activity. Several are designated aminopeptidase N, EC 3.4.11.2, after the Escherichia coli enzyme, suggesting a similar activity profile. This family consists of all aminopeptidases closely related to E. coli PepN and presumed to have similar (not identical) function. Nearly all are found in Proteobacteria, but members are found also in Cyanobacteria, plants, and apicomplexan parasites. This family differs greatly in sequence from the family of aminopeptidases typified by Streptomyces lividans PepN (TIGR02412), from the membrane bound aminopeptidase N family in animals, etc.
Probab=56.40 E-value=6 Score=43.37 Aligned_cols=20 Identities=40% Similarity=0.556 Sum_probs=17.2
Q ss_pred CHHHHHHHHHHHhhhcCCCC
Q 022290 47 PYEQILDTMLHELCHNEYGP 66 (299)
Q Consensus 47 p~~~i~~v~lHELaH~~~~~ 66 (299)
.+..|..|+.|||+|.+.||
T Consensus 279 ~~~~i~~VIaHElaHqWfGN 298 (863)
T TIGR02414 279 DYERIESVIAHEYFHNWTGN 298 (863)
T ss_pred HHHHHHHHHHHHHHHHHhcc
Confidence 35678999999999999985
No 88
>cd00203 ZnMc Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease.
Probab=55.86 E-value=5.9 Score=33.33 Aligned_cols=22 Identities=32% Similarity=0.247 Sum_probs=19.1
Q ss_pred HHHHHHHHHHhhhcCCCCCChh
Q 022290 49 EQILDTMLHELCHNEYGPHNAD 70 (299)
Q Consensus 49 ~~i~~v~lHELaH~~~~~H~~~ 70 (299)
.....|++|||.|.+-..|+..
T Consensus 94 ~~~~~~~~HElGH~LGl~H~~~ 115 (167)
T cd00203 94 KEGAQTIAHELGHALGFYHDHD 115 (167)
T ss_pred ccchhhHHHHHHHHhCCCccCc
Confidence 4578999999999999999865
No 89
>PF15639 Tox-MPTase3: Metallopeptidase toxin 3
Probab=55.83 E-value=4.8 Score=34.44 Aligned_cols=34 Identities=26% Similarity=0.222 Sum_probs=22.5
Q ss_pred CCcEEEEEecCCCCCCCCCC-------HHHHHHHHHHHhhhc
Q 022290 28 GGAEVKLRLRRPNREWDFFP-------YEQILDTMLHELCHN 62 (299)
Q Consensus 28 ~G~~I~LrLR~~~~~~~f~p-------~~~i~~v~lHELaH~ 62 (299)
++++|.|+-.+..+. .-.| +-.|..||||||.|-
T Consensus 71 ~~~~i~I~~~lV~~~-Ek~~~~~r~~~~~~v~~TlLHEliHw 111 (135)
T PF15639_consen 71 GSQVIRIDGDLVNMF-EKGPGERRAGNVYLVGSTLLHELIHW 111 (135)
T ss_pred CCcEEEeeHHHhhhh-hcCCcccccceEEEeehHHHHHHHHh
Confidence 367887777665422 2222 235779999999995
No 90
>PRK14015 pepN aminopeptidase N; Provisional
Probab=55.65 E-value=5.7 Score=43.61 Aligned_cols=19 Identities=42% Similarity=0.597 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHhhhcCCCC
Q 022290 48 YEQILDTMLHELCHNEYGP 66 (299)
Q Consensus 48 ~~~i~~v~lHELaH~~~~~ 66 (299)
+..|..||+|||+|.+.||
T Consensus 293 ~~~i~~vIaHElaHqWFGN 311 (875)
T PRK14015 293 YERIESVIAHEYFHNWTGN 311 (875)
T ss_pred HHHHHHHHHHHHHHHHHhC
Confidence 3468899999999999885
No 91
>cd04268 ZnMc_MMP_like Zinc-dependent metalloprotease, MMP_like subfamily. This group contains matrix metalloproteinases (MMPs), serralysins, and the astacin_like family of proteases.
Probab=54.89 E-value=8.9 Score=32.28 Aligned_cols=22 Identities=32% Similarity=0.240 Sum_probs=19.4
Q ss_pred HHHHHHHHHHhhhcCCCCCChh
Q 022290 49 EQILDTMLHELCHNEYGPHNAD 70 (299)
Q Consensus 49 ~~i~~v~lHELaH~~~~~H~~~ 70 (299)
..+..|++|||-|.+-..|+..
T Consensus 92 ~~~~~~~~HEiGHaLGL~H~~~ 113 (165)
T cd04268 92 ARLRNTAEHELGHALGLRHNFA 113 (165)
T ss_pred HHHHHHHHHHHHHHhcccccCc
Confidence 4688999999999999888875
No 92
>PF13058 DUF3920: Protein of unknown function (DUF3920)
Probab=54.63 E-value=5.4 Score=33.42 Aligned_cols=20 Identities=45% Similarity=0.693 Sum_probs=17.1
Q ss_pred CCCHHHHHHHHHHHhhhcCC
Q 022290 45 FFPYEQILDTMLHELCHNEY 64 (299)
Q Consensus 45 f~p~~~i~~v~lHELaH~~~ 64 (299)
|-.|+.|..|++||+-|-..
T Consensus 70 we~y~qvlktllhefrh~mQ 89 (126)
T PF13058_consen 70 WEEYEQVLKTLLHEFRHAMQ 89 (126)
T ss_pred hHHHHHHHHHHHHHHHHHHH
Confidence 45689999999999999765
No 93
>PRK04023 DNA polymerase II large subunit; Validated
Probab=54.57 E-value=14 Score=41.21 Aligned_cols=53 Identities=21% Similarity=0.483 Sum_probs=37.9
Q ss_pred CCCccCCccccccccCCccccccCCCCCCCCCCCCCcccCCcccccCCCCccccccCCCCCCC
Q 022290 224 GQMWQCNMCTLLNQPLALTCEACGTQRNKSVGNLKGWSCKFCTLDNSSLSERCLACGEWRYSN 286 (299)
Q Consensus 224 ~~~W~C~~CT~~N~~~a~~C~aCgt~rp~~~~~~~~W~C~~Ct~~N~~~~~~C~~Cg~~r~~~ 286 (299)
.+.=.|+.|.-. .....|..||.. ....|.|+.|...... ..|..|+....+.
T Consensus 624 Vg~RfCpsCG~~--t~~frCP~CG~~------Te~i~fCP~CG~~~~~--y~CPKCG~El~~~ 676 (1121)
T PRK04023 624 IGRRKCPSCGKE--TFYRRCPFCGTH------TEPVYRCPRCGIEVEE--DECEKCGREPTPY 676 (1121)
T ss_pred ccCccCCCCCCc--CCcccCCCCCCC------CCcceeCccccCcCCC--CcCCCCCCCCCcc
Confidence 356789999876 355679999976 2346899999766443 5699999876543
No 94
>COG4324 Predicted aminopeptidase [General function prediction only]
Probab=54.35 E-value=21 Score=34.53 Aligned_cols=48 Identities=17% Similarity=0.205 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHHHhhhcC-CCCCChhHHHHHHHHHHHHHHHHHccccCC
Q 022290 46 FPYEQILDTMLHELCHNE-YGPHNADFYKLWDEIRKECDELMAKGITGT 93 (299)
Q Consensus 46 ~p~~~i~~v~lHELaH~~-~~~H~~~F~~l~~~l~~e~~~l~~~G~~g~ 93 (299)
.|-+.|-..|.|||+|-+ +-+.|..|-+-.......--.-.+.-++|+
T Consensus 192 ~dd~~lA~LIFHELAHQk~Y~~~DtAFNEsFAtaVEt~Gvr~Wl~~~g~ 240 (376)
T COG4324 192 QDDTYLASLIFHELAHQKIYVNNDTAFNESFATAVETSGVRKWLRATGD 240 (376)
T ss_pred CChHHHHHHHHHHHhhheEeecCcchHhHHHHHHHHHHhHHHHHHhcCC
Confidence 355778899999999987 668888887776665554444444445543
No 95
>PF01433 Peptidase_M1: Peptidase family M1 This is family M1 in the peptidase classification.; InterPro: IPR014782 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M1 (clan MA(E)), the type example being aminopeptidase N from Homo sapiens (Human). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. Membrane alanine aminopeptidase (3.4.11.2 from EC) is part of the HEXXH+E group; it consists entirely of aminopeptidases, spread across a wide variety of species []. Functional studies show that CD13/APN catalyzes the removal of single amino acids from the amino terminus of small peptides and probably plays a role in their final digestion; one family member (leukotriene-A4 hydrolase) is known to hydrolyse the epoxide leukotriene-A4 to form an inflammatory mediator []. This hydrolase has been shown to have aminopeptidase activity [], and the zinc ligands of the M1 family were identified by site-directed mutagenesis on this enzyme [] CD13 participates in trimming peptides bound to MHC class II molecules [] and cleaves MIP-1 chemokine, which alters target cell specificity from basophils to eosinophils []. CD13 acts as a receptor for specific strains of RNA viruses (coronaviruses) which cause a relatively large percentage of upper respiratory trace infections. CD molecules are leucocyte antigens on cell surfaces. CD antigens nomenclature is updated at Protein Reviews On The Web (http://prow.nci.nih.gov/). ; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding; PDB: 2XQ0_A 2XPY_A 2XPZ_A 3SE6_B 3EBH_A 3EBG_A 3T8V_A 3Q44_A 3Q43_A 3EBI_A ....
Probab=53.85 E-value=10 Score=36.38 Aligned_cols=19 Identities=32% Similarity=0.560 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHhhhcCCCC
Q 022290 48 YEQILDTMLHELCHNEYGP 66 (299)
Q Consensus 48 ~~~i~~v~lHELaH~~~~~ 66 (299)
...+..+|+|||+|...|+
T Consensus 292 ~~~~~~~iahElahqWfGn 310 (390)
T PF01433_consen 292 KQEIASLIAHELAHQWFGN 310 (390)
T ss_dssp HHHHHHHHHHHHHTTTBTT
T ss_pred hhhhHHHHHHHHHHHHhcc
Confidence 4578999999999999986
No 96
>PF10023 DUF2265: Predicted aminopeptidase (DUF2265); InterPro: IPR014553 This group represents a predicted aminopeptidase.
Probab=53.46 E-value=22 Score=34.98 Aligned_cols=41 Identities=17% Similarity=0.336 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHHHHhhhcC-CCCCChhHHHHHHHHHHHHHHH
Q 022290 45 FFPYEQILDTMLHELCHNE-YGPHNADFYKLWDEIRKECDEL 85 (299)
Q Consensus 45 f~p~~~i~~v~lHELaH~~-~~~H~~~F~~l~~~l~~e~~~l 85 (299)
-.|...+..+|+|||+|-+ +-+-|..|=+-+..+..+.-..
T Consensus 159 ~~~~~~LA~LIfHELaHq~~Yv~~dt~FNEsfAtfVe~~G~~ 200 (337)
T PF10023_consen 159 RYPDGELARLIFHELAHQTLYVKGDTAFNESFATFVEREGAR 200 (337)
T ss_pred CCCchHHHHHHHHHHhhceeecCCCchhhHHHHHHHHHHHHH
Confidence 3566789999999999987 5577778888777776655333
No 97
>TIGR02412 pepN_strep_liv aminopeptidase N, Streptomyces lividans type. This family is a subset of the members of the zinc metallopeptidase family M1 (pfam01433), with a single member characterized in Streptomyces lividans 66 and designated aminopeptidase N. The spectrum of activity may differ somewhat from the aminopeptidase N clade of E. coli and most other Proteobacteria, well separated phylogenetically within the M1 family. The M1 family also includes leukotriene A-4 hydrolase/aminopeptidase (with a bifunctional active site).
Probab=52.50 E-value=8.1 Score=41.99 Aligned_cols=19 Identities=32% Similarity=0.503 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHhhhcCCCC
Q 022290 48 YEQILDTMLHELCHNEYGP 66 (299)
Q Consensus 48 ~~~i~~v~lHELaH~~~~~ 66 (299)
...+..||+|||+|..+||
T Consensus 284 ~~~~~~viaHElAHqWFGn 302 (831)
T TIGR02412 284 KENRAGVILHEMAHMWFGD 302 (831)
T ss_pred HHHHHHHHHHHHHHHHhCC
Confidence 3467899999999999883
No 98
>cd04277 ZnMc_serralysin_like Zinc-dependent metalloprotease, serralysin_like subfamily. Serralysins and related proteases are important virulence factors in pathogenic bacteria. They may be secreted into the medium via a mechanism found in gram-negative bacteria, that does not require n-terminal signal sequences which are cleaved after the transmembrane translocation. A calcium-binding domain c-terminal to the metalloprotease domain, which contains multiple tandem repeats of a nine-residue motif including the pattern GGxGxD, and which forms a parallel beta roll may be involved in the translocation mechanism and/or substrate binding. Serralysin family members may have a broad spectrum of substrates each, including host immunoglobulins, complement proteins, cell matrix and cytoskeletal proteins, as well as antimicrobial peptides.
Probab=52.25 E-value=17 Score=31.75 Aligned_cols=38 Identities=16% Similarity=0.095 Sum_probs=26.3
Q ss_pred cEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCCCCh
Q 022290 30 AEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGPHNA 69 (299)
Q Consensus 30 ~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~H~~ 69 (299)
..|.|+...... ...+-....+|++|||-|.+--.|.-
T Consensus 94 g~i~~~~~~~~~--~~~~g~~~~~t~~HEiGHaLGL~H~~ 131 (186)
T cd04277 94 GDIWFNSSYDTN--SDSPGSYGYQTIIHEIGHALGLEHPG 131 (186)
T ss_pred ceeEEecCcccc--cCCCChhhHHHHHHHHHHHhcCCCCC
Confidence 358888665321 11345667899999999998777654
No 99
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=52.16 E-value=4.7 Score=43.93 Aligned_cols=51 Identities=22% Similarity=0.501 Sum_probs=0.0
Q ss_pred CCccCCccccccccCCccccccCCCCCCCCCCCCCcccCCcccccCCCCccccccCCCCCC
Q 022290 225 QMWQCNMCTLLNQPLALTCEACGTQRNKSVGNLKGWSCKFCTLDNSSLSERCLACGEWRYS 285 (299)
Q Consensus 225 ~~W~C~~CT~~N~~~a~~C~aCgt~rp~~~~~~~~W~C~~Ct~~N~~~~~~C~~Cg~~r~~ 285 (299)
..-.|+.|... .....|..||+.. ...|.|+.|....... .|..|+..-.+
T Consensus 654 ~~r~Cp~Cg~~--t~~~~Cp~CG~~T------~~~~~Cp~C~~~~~~~--~C~~C~~~~~~ 704 (900)
T PF03833_consen 654 GRRRCPKCGKE--TFYNRCPECGSHT------EPVYVCPDCGIEVEED--ECPKCGRETTS 704 (900)
T ss_dssp -------------------------------------------------------------
T ss_pred ecccCcccCCc--chhhcCcccCCcc------ccceeccccccccCcc--ccccccccCcc
Confidence 46789999876 4445899999762 3379999999876655 99999986443
No 100
>PF10460 Peptidase_M30: Peptidase M30; InterPro: IPR019501 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This family contains metallopeptidases belonging to MEROPS peptidase family M30 (hyicolysin family, clan MA). Hyicolysin has a zinc ion which is liganded by two histidine and one glutamate residue.
Probab=51.60 E-value=7 Score=38.82 Aligned_cols=41 Identities=10% Similarity=-0.107 Sum_probs=25.3
Q ss_pred ecCCCcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCC
Q 022290 25 NIGGGAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGP 66 (299)
Q Consensus 25 N~n~G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~ 66 (299)
..|.++.+.|........ ...-.+.+..||+||+-|+++-+
T Consensus 114 ~SNe~e~~YiD~~~~~~~-~~~~~~~~~sTlAHEfQHmInfy 154 (366)
T PF10460_consen 114 YSNESEYFYIDSETLYLG-GNSGPDTVYSTLAHEFQHMINFY 154 (366)
T ss_pred CCcceeEEEEecHHhhcc-CCccHHHHHHHHHHHHHHHHHHH
Confidence 345566566655431100 01126789999999999999654
No 101
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=50.82 E-value=9.1 Score=27.32 Aligned_cols=25 Identities=28% Similarity=0.493 Sum_probs=19.8
Q ss_pred CCccCCccccccccCCccccccCCC
Q 022290 225 QMWQCNMCTLLNQPLALTCEACGTQ 249 (299)
Q Consensus 225 ~~W~C~~CT~~N~~~a~~C~aCgt~ 249 (299)
..+.|-.|.-.|++.+..|-.||..
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~~ 37 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGYK 37 (48)
T ss_pred cccchhcccCCCCccccccccCCCC
Confidence 4678888888888888888888753
No 102
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=50.13 E-value=7.8 Score=26.09 Aligned_cols=13 Identities=46% Similarity=1.219 Sum_probs=6.7
Q ss_pred CCcccCCcccccC
Q 022290 258 KGWSCKFCTLDNS 270 (299)
Q Consensus 258 ~~W~C~~Ct~~N~ 270 (299)
..|.|.+|...|.
T Consensus 23 ~~w~C~~C~~~N~ 35 (40)
T PF04810_consen 23 KTWICNFCGTKNP 35 (40)
T ss_dssp TEEEETTT--EEE
T ss_pred CEEECcCCCCcCC
Confidence 4566666666654
No 103
>TIGR02411 leuko_A4_hydro leukotriene A-4 hydrolase/aminopeptidase. Members of this family represent a distinctive subset within the zinc metallopeptidase family M1 (pfam01433). The majority of the members of pfam01433 are aminopeptidases, but the sequences in this family for which the function is known are leukotriene A-4 hydrolase. A dual epoxide hydrolase and aminopeptidase activity at the same active site is indicated. The physiological substrate for aminopeptidase activity is not known.
Probab=50.08 E-value=11 Score=39.69 Aligned_cols=16 Identities=38% Similarity=0.532 Sum_probs=14.0
Q ss_pred HHHHHHHHhhhcCCCC
Q 022290 51 ILDTMLHELCHNEYGP 66 (299)
Q Consensus 51 i~~v~lHELaH~~~~~ 66 (299)
...||+|||||...||
T Consensus 279 ~~~viaHElAHqWfGN 294 (601)
T TIGR02411 279 NVDVIAHELAHSWSGN 294 (601)
T ss_pred hhhhHHHHHHhhccCc
Confidence 4579999999999984
No 104
>cd04279 ZnMc_MMP_like_1 Zinc-dependent metalloprotease; MMP_like sub-family 1. A group of bacterial, archaeal, and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=50.01 E-value=12 Score=31.79 Aligned_cols=23 Identities=35% Similarity=0.289 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHhhhcCCCCCChh
Q 022290 48 YEQILDTMLHELCHNEYGPHNAD 70 (299)
Q Consensus 48 ~~~i~~v~lHELaH~~~~~H~~~ 70 (299)
...+..|++|||-|.+--.|...
T Consensus 101 ~~~~~~~~~HEiGHaLGL~H~~~ 123 (156)
T cd04279 101 AENLQAIALHELGHALGLWHHSD 123 (156)
T ss_pred chHHHHHHHHHhhhhhcCCCCCC
Confidence 35788999999999998888765
No 105
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=47.01 E-value=12 Score=35.41 Aligned_cols=28 Identities=21% Similarity=0.699 Sum_probs=19.5
Q ss_pred CCCCcccCCcccccCCCCccccccCCCC
Q 022290 256 NLKGWSCKFCTLDNSSLSERCLACGEWR 283 (299)
Q Consensus 256 ~~~~W~C~~Ct~~N~~~~~~C~~Cg~~r 283 (299)
....|.|..|++....-.+.|..|+++-
T Consensus 351 ~~p~~~c~~cg~~~~~~~~~c~~c~~~~ 378 (389)
T PRK11788 351 RKPRYRCRNCGFTARTLYWHCPSCKAWE 378 (389)
T ss_pred CCCCEECCCCCCCCccceeECcCCCCcc
Confidence 3445777777777777777777777653
No 106
>PRK14873 primosome assembly protein PriA; Provisional
Probab=45.81 E-value=14 Score=39.47 Aligned_cols=50 Identities=22% Similarity=0.487 Sum_probs=31.6
Q ss_pred ccCCccccccccCCccccccCCCCCCCCCCCCCcccCCcccccCCCCccccccCCCCC
Q 022290 227 WQCNMCTLLNQPLALTCEACGTQRNKSVGNLKGWSCKFCTLDNSSLSERCLACGEWRY 284 (299)
Q Consensus 227 W~C~~CT~~N~~~a~~C~aCgt~rp~~~~~~~~W~C~~Ct~~N~~~~~~C~~Cg~~r~ 284 (299)
=.|..|.. ...|..|..+-... ...+.-.|+.|++.- ..+.|..||....
T Consensus 384 l~C~~Cg~-----~~~C~~C~~~L~~h-~~~~~l~Ch~CG~~~--~p~~Cp~Cgs~~l 433 (665)
T PRK14873 384 LACARCRT-----PARCRHCTGPLGLP-SAGGTPRCRWCGRAA--PDWRCPRCGSDRL 433 (665)
T ss_pred eEhhhCcC-----eeECCCCCCceeEe-cCCCeeECCCCcCCC--cCccCCCCcCCcc
Confidence 35666643 24566666542211 234567899999963 4789999998643
No 107
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=45.39 E-value=12 Score=33.30 Aligned_cols=23 Identities=22% Similarity=0.592 Sum_probs=12.5
Q ss_pred CccccccCCCCCCCCCCCCCcccCCcc
Q 022290 240 ALTCEACGTQRNKSVGNLKGWSCKFCT 266 (299)
Q Consensus 240 a~~C~aCgt~rp~~~~~~~~W~C~~Ct 266 (299)
.-.|.+||-.-- ....|.|+.|.
T Consensus 134 ~~vC~vCGy~~~----ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYTHE----GEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCccc----CCCCCcCCCCC
Confidence 446777774421 12356666665
No 108
>smart00235 ZnMc Zinc-dependent metalloprotease. Neutral zinc metallopeptidases. This alignment represents a subset of known subfamilies. Highest similarity occurs in the HExxH zinc-binding site/ active site.
Probab=44.92 E-value=10 Score=31.35 Aligned_cols=18 Identities=28% Similarity=0.158 Sum_probs=15.4
Q ss_pred HHHHHHhhhcCCCCCChh
Q 022290 53 DTMLHELCHNEYGPHNAD 70 (299)
Q Consensus 53 ~v~lHELaH~~~~~H~~~ 70 (299)
.|++|||.|.+-..|+..
T Consensus 88 ~~~~HEigHaLGl~H~~~ 105 (140)
T smart00235 88 GVAAHELGHALGLYHEQS 105 (140)
T ss_pred ccHHHHHHHHhcCCcCCC
Confidence 599999999998888764
No 109
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=44.89 E-value=14 Score=26.42 Aligned_cols=24 Identities=25% Similarity=0.535 Sum_probs=22.5
Q ss_pred CCcccCCcccccCCCCccccccCC
Q 022290 258 KGWSCKFCTLDNSSLSERCLACGE 281 (299)
Q Consensus 258 ~~W~C~~Ct~~N~~~~~~C~~Cg~ 281 (299)
..+.|..|...|+..+..|--||.
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 578999999999999999999996
No 110
>KOG1046 consensus Puromycin-sensitive aminopeptidase and related aminopeptidases [Amino acid transport and metabolism; Posttranslational modification, protein turnover, chaperones]
Probab=44.80 E-value=13 Score=40.92 Aligned_cols=19 Identities=26% Similarity=0.602 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHhhhcCCCC
Q 022290 48 YEQILDTMLHELCHNEYGP 66 (299)
Q Consensus 48 ~~~i~~v~lHELaH~~~~~ 66 (299)
+..|..||+|||||-++||
T Consensus 321 k~~va~vIaHElAHQWFGN 339 (882)
T KOG1046|consen 321 KQRVAEVIAHELAHQWFGN 339 (882)
T ss_pred HHHHHHHHHHHHHHHHhcC
Confidence 6779999999999999997
No 111
>PF13583 Reprolysin_4: Metallo-peptidase family M12B Reprolysin-like
Probab=44.79 E-value=12 Score=33.81 Aligned_cols=18 Identities=39% Similarity=0.418 Sum_probs=17.1
Q ss_pred HHHHHHhhhcCCCCCChh
Q 022290 53 DTMLHELCHNEYGPHNAD 70 (299)
Q Consensus 53 ~v~lHELaH~~~~~H~~~ 70 (299)
+|++|||-|+.--.|+..
T Consensus 139 ~~~aHEiGH~lGl~H~~~ 156 (206)
T PF13583_consen 139 QTFAHEIGHNLGLRHDFD 156 (206)
T ss_pred hHHHHHHHHHhcCCCCcc
Confidence 789999999999999988
No 112
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=44.46 E-value=8.5 Score=36.98 Aligned_cols=41 Identities=29% Similarity=0.693 Sum_probs=22.4
Q ss_pred CccCCccc-------cccccCCccccccCCC------C-CCCCCCCCCcccCCcc
Q 022290 226 MWQCNMCT-------LLNQPLALTCEACGTQ------R-NKSVGNLKGWSCKFCT 266 (299)
Q Consensus 226 ~W~C~~CT-------~~N~~~a~~C~aCgt~------r-p~~~~~~~~W~C~~Ct 266 (299)
-|.|--|- -.|.-..+.|+-|..- . |-...+++.|+|+-|.
T Consensus 275 rwqcieck~csicgtsenddqllfcddcdrgyhmyclsppm~eppegswsc~KOG 329 (336)
T KOG1244|consen 275 RWQCIECKYCSICGTSENDDQLLFCDDCDRGYHMYCLSPPMVEPPEGSWSCHLCL 329 (336)
T ss_pred eeeeeecceeccccCcCCCceeEeecccCCceeeEecCCCcCCCCCCchhHHHHH
Confidence 38776663 2344444555555421 0 1112467889999886
No 113
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=44.06 E-value=13 Score=22.98 Aligned_cols=22 Identities=23% Similarity=0.522 Sum_probs=14.9
Q ss_pred ccCCcccccCCCCccccccCCC
Q 022290 261 SCKFCTLDNSSLSERCLACGEW 282 (299)
Q Consensus 261 ~C~~Ct~~N~~~~~~C~~Cg~~ 282 (299)
.|+.|.-.-......|..||..
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCC
Confidence 4667776667777777777653
No 114
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=43.73 E-value=19 Score=26.44 Aligned_cols=29 Identities=28% Similarity=0.521 Sum_probs=21.3
Q ss_pred CcccCCcccccCCCCccccccCCCCCCCCCC
Q 022290 259 GWSCKFCTLDNSSLSERCLACGEWRYSNGPP 289 (299)
Q Consensus 259 ~W~C~~Ct~~N~~~~~~C~~Cg~~r~~~~pp 289 (299)
.-.|..|....- ...|..||.+-.+.-||
T Consensus 5 mr~C~~CgvYTL--k~~CP~CG~~t~~~~P~ 33 (56)
T PRK13130 5 IRKCPKCGVYTL--KEICPVCGGKTKNPHPP 33 (56)
T ss_pred ceECCCCCCEEc--cccCcCCCCCCCCCCCC
Confidence 346888876665 78899999987766553
No 115
>KOG3658 consensus Tumor necrosis factor-alpha-converting enzyme (TACE/ADAM17) and related metalloproteases [Extracellular structures]
Probab=42.19 E-value=15 Score=39.27 Aligned_cols=46 Identities=24% Similarity=0.220 Sum_probs=34.3
Q ss_pred cCCCcEEEEEecCCC--CCCCCCCHHHHHHHHHHHhhhcCCCCCChhH
Q 022290 26 IGGGAEVKLRLRRPN--REWDFFPYEQILDTMLHELCHNEYGPHNADF 71 (299)
Q Consensus 26 ~n~G~~I~LrLR~~~--~~~~f~p~~~i~~v~lHELaH~~~~~H~~~F 71 (299)
+|.|.++.||.-+.. +...-.|..+.+-|++||+-||.-.+||..=
T Consensus 365 y~~G~~~sLNtGi~T~~NYg~~Vp~kvs~lt~AHEiGHNfGSpHDp~~ 412 (764)
T KOG3658|consen 365 YNEGKKRSLNTGISTSVNYGKRVPTKVSDLTLAHEIGHNFGSPHDPDI 412 (764)
T ss_pred ccCcceEEeecceeeeeecCCccCcchhheeehhhhccccCCCCCCCC
Confidence 444667777654322 2345688999999999999999999999753
No 116
>KOG3607 consensus Meltrins, fertilins and related Zn-dependent metalloproteinases of the ADAMs family [Posttranslational modification, protein turnover, chaperones]
Probab=41.94 E-value=15 Score=39.69 Aligned_cols=22 Identities=27% Similarity=0.187 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHhhhcCCCCCCh
Q 022290 48 YEQILDTMLHELCHNEYGPHNA 69 (299)
Q Consensus 48 ~~~i~~v~lHELaH~~~~~H~~ 69 (299)
+..+..||+|||.|++-+.||.
T Consensus 320 ~~~~a~v~AhelgH~lGm~hD~ 341 (716)
T KOG3607|consen 320 LLAFAVVLAHELGHNLGMIHDE 341 (716)
T ss_pred chhHHHHHHHHHHhhcCccccc
Confidence 4567789999999999999999
No 117
>PF10463 Peptidase_U49: Peptidase U49; InterPro: IPR019504 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 families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This entry contains peptidases belonging to MEROPS peptidase family U49 (Lit peptidase, clan U-). The Lit peptidase from Escherichia coli functions in bacterial cell death in response to infection by Enterobacteria phage T4. Following binding of Gol peptide to domains II and III of elongation factor Tu, the Lit peptidase cleaves domain I of the elongation factor. This prevents binding of guanine nucleotides, shuts down translation and leads to cell death.
Probab=41.89 E-value=17 Score=33.27 Aligned_cols=19 Identities=37% Similarity=0.466 Sum_probs=14.1
Q ss_pred HHHHHHHHhhhcCCCCCCh
Q 022290 51 ILDTMLHELCHNEYGPHNA 69 (299)
Q Consensus 51 i~~v~lHELaH~~~~~H~~ 69 (299)
+-.+|+||++|++++.=..
T Consensus 101 ~~fil~HE~~Hv~~~h~~~ 119 (206)
T PF10463_consen 101 IAFILLHELAHVVLGHEGD 119 (206)
T ss_pred HHHHHHHHHHHHHHcCccc
Confidence 4578999999977664443
No 118
>PRK13267 archaemetzincin-like protein; Reviewed
Probab=41.79 E-value=20 Score=32.03 Aligned_cols=23 Identities=26% Similarity=0.241 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHhhhcCCCCCChh
Q 022290 48 YEQILDTMLHELCHNEYGPHNAD 70 (299)
Q Consensus 48 ~~~i~~v~lHELaH~~~~~H~~~ 70 (299)
.+.+..+++|||.|+.-..|-..
T Consensus 122 ~~R~~k~~~HElGH~lGL~HC~~ 144 (179)
T PRK13267 122 EERVRKEVTHELGHTLGLEHCDN 144 (179)
T ss_pred HHHHHHHHHHHHHHHcCCccCCC
Confidence 45667789999999999999544
No 119
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=41.63 E-value=21 Score=38.60 Aligned_cols=49 Identities=18% Similarity=0.608 Sum_probs=36.5
Q ss_pred ccCCccccccccCCccccccCCCCCCCCCCCCCcccCCcccccCCCCccccccCCC
Q 022290 227 WQCNMCTLLNQPLALTCEACGTQRNKSVGNLKGWSCKFCTLDNSSLSERCLACGEW 282 (299)
Q Consensus 227 W~C~~CT~~N~~~a~~C~aCgt~rp~~~~~~~~W~C~~Ct~~N~~~~~~C~~Cg~~ 282 (299)
=.|..|.++ ..|..|..+-.-. ...+.-.|+.|++. ...-..|..||..
T Consensus 436 l~C~~Cg~v-----~~Cp~Cd~~lt~H-~~~~~L~CH~Cg~~-~~~p~~Cp~Cgs~ 484 (730)
T COG1198 436 LLCRDCGYI-----AECPNCDSPLTLH-KATGQLRCHYCGYQ-EPIPQSCPECGSE 484 (730)
T ss_pred eecccCCCc-----ccCCCCCcceEEe-cCCCeeEeCCCCCC-CCCCCCCCCCCCC
Confidence 468888654 5788888652211 34467899999999 8888999999986
No 120
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=41.01 E-value=30 Score=39.56 Aligned_cols=50 Identities=20% Similarity=0.391 Sum_probs=33.0
Q ss_pred CccccccCCCCCCCCCCCCCcccCCcccccCCCCccccccCCCCCCCCCCCCCCCCCCC
Q 022290 240 ALTCEACGTQRNKSVGNLKGWSCKFCTLDNSSLSERCLACGEWRYSNGPPISTPGPYPG 298 (299)
Q Consensus 240 a~~C~aCgt~rp~~~~~~~~W~C~~Ct~~N~~~~~~C~~Cg~~r~~~~pp~~~~~~~~~ 298 (299)
..+|..|++.-+ ...|+.|+....... .|..||..-.+.... ++.+|+-|
T Consensus 667 ~rkCPkCG~~t~-------~~fCP~CGs~te~vy-~CPsCGaev~~des~-a~~CP~CG 716 (1337)
T PRK14714 667 RRRCPSCGTETY-------ENRCPDCGTHTEPVY-VCPDCGAEVPPDESG-RVECPRCD 716 (1337)
T ss_pred EEECCCCCCccc-------cccCcccCCcCCCce-eCccCCCccCCCccc-cccCCCCC
Confidence 467999998643 358999998876544 899999965443211 44454443
No 121
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=40.45 E-value=7.6 Score=37.35 Aligned_cols=49 Identities=20% Similarity=0.444 Sum_probs=30.8
Q ss_pred ccccCCccccccCCCCCCCCC-------CCCCcccCCcccccCCCCccccccCCCCC
Q 022290 235 LNQPLALTCEACGTQRNKSVG-------NLKGWSCKFCTLDNSSLSERCLACGEWRY 284 (299)
Q Consensus 235 ~N~~~a~~C~aCgt~rp~~~~-------~~~~W~C~~Ct~~N~~~~~~C~~Cg~~r~ 284 (299)
.| .+...|-+||+..-.+.. .-.--.|+.|-..=.--..+|+.|++.+.
T Consensus 181 e~-e~~~~CPvCGS~PvaSmV~~g~~~~GlRYL~CslC~teW~~VR~KC~nC~~t~~ 236 (308)
T COG3058 181 EN-ESRQYCPVCGSMPVASMVQIGETEQGLRYLHCSLCETEWHYVRVKCSNCEQSKK 236 (308)
T ss_pred cc-cccccCCCcCCCCcceeeeecCccccchhhhhhhHHHHHHHHHHHhccccccCC
Confidence 44 455678888865333321 11234688888777777788888888764
No 122
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=39.64 E-value=14 Score=37.57 Aligned_cols=29 Identities=14% Similarity=0.179 Sum_probs=18.9
Q ss_pred CCCcccCCcccccCC-------------------CCccccccCCCCCC
Q 022290 257 LKGWSCKFCTLDNSS-------------------LSERCLACGEWRYS 285 (299)
Q Consensus 257 ~~~W~C~~Ct~~N~~-------------------~~~~C~~Cg~~r~~ 285 (299)
...|.|..|+|.=.+ ..|+|..|+.+|..
T Consensus 423 ~~~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~k~~ 470 (479)
T PRK05452 423 GPRMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLGKDV 470 (479)
T ss_pred CCeEEECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCcHHH
Confidence 345777777765443 36788888877653
No 123
>PF01457 Peptidase_M8: Leishmanolysin This Prosite motif covers only the active site. This is family M8 in the peptidase classification. ; InterPro: IPR001577 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M8 (leishmanolysin family, clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. Leishmanolysin is an enzyme found in the eukaryotes including Leishmania and related parasitic protozoa []. The endopeptidase is the most abundant protein on the cell surface during the promastigote stage of the parasite, and is attached to the membrane by a glycosylphosphatidylinositol anchor []. In the amastigote form, the parasite lives in lysosomes of host macrophages, producing a form of the protease that has an acidic pH optimum []. This differs from most other metalloproteases and may be an adaptation to the environment in which the organism survives [].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis, 0007155 cell adhesion, 0016020 membrane; PDB: 1LML_A.
Probab=39.00 E-value=22 Score=36.56 Aligned_cols=32 Identities=16% Similarity=0.273 Sum_probs=18.4
Q ss_pred EEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCC
Q 022290 31 EVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGP 66 (299)
Q Consensus 31 ~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~ 66 (299)
.|.|+...-.. + ......+|++|||+|.+-..
T Consensus 194 ~in~~p~~i~~---~-~~~~~~~~~~HEi~HaLGFs 225 (521)
T PF01457_consen 194 VININPSYIPS---F-YFQEFFRTVIHEIAHALGFS 225 (521)
T ss_dssp EEE--GGG------S---HHHHHHHHHHHHHHTT-S
T ss_pred EEEEchhHccc---h-hhhcccceeeeeeeeeeeec
Confidence 36666554221 1 46788899999999998543
No 124
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=38.97 E-value=24 Score=36.28 Aligned_cols=51 Identities=20% Similarity=0.528 Sum_probs=31.5
Q ss_pred CccCCccccccccCCccccccCCCCCCCCCCCCCcccCCcccccCCCCccccccCCCC
Q 022290 226 MWQCNMCTLLNQPLALTCEACGTQRNKSVGNLKGWSCKFCTLDNSSLSERCLACGEWR 283 (299)
Q Consensus 226 ~W~C~~CT~~N~~~a~~C~aCgt~rp~~~~~~~~W~C~~Ct~~N~~~~~~C~~Cg~~r 283 (299)
.-.|..|.. ...|..|+.+-.-. .....-.|+.|++.-... +.|..|+...
T Consensus 213 ~~~C~~Cg~-----~~~C~~C~~~l~~h-~~~~~l~Ch~Cg~~~~~~-~~Cp~C~s~~ 263 (505)
T TIGR00595 213 NLLCRSCGY-----ILCCPNCDVSLTYH-KKEGKLRCHYCGYQEPIP-KTCPQCGSED 263 (505)
T ss_pred eeEhhhCcC-----ccCCCCCCCceEEe-cCCCeEEcCCCcCcCCCC-CCCCCCCCCe
Confidence 356777754 35677777542211 234467788888765544 5888888754
No 125
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=38.20 E-value=15 Score=33.86 Aligned_cols=27 Identities=22% Similarity=0.464 Sum_probs=16.7
Q ss_pred ccccccCCCCCCCCCCCCCcccCCcccccCCCC
Q 022290 241 LTCEACGTQRNKSVGNLKGWSCKFCTLDNSSLS 273 (299)
Q Consensus 241 ~~C~aCgt~rp~~~~~~~~W~C~~Ct~~N~~~~ 273 (299)
..|..||. .....|.|+.|++......
T Consensus 310 ~~C~~cg~------~~~r~~~C~~cg~~~~rD~ 336 (364)
T COG0675 310 KTCPCCGH------LSGRLFKCPRCGFVHDRDV 336 (364)
T ss_pred ccccccCC------ccceeEECCCCCCeehhhH
Confidence 34556655 1234688888888766553
No 126
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=37.77 E-value=21 Score=26.13 Aligned_cols=29 Identities=24% Similarity=0.622 Sum_probs=16.6
Q ss_pred ccccccCCCCCCCCCCCCCcccCCcccccC
Q 022290 241 LTCEACGTQRNKSVGNLKGWSCKFCTLDNS 270 (299)
Q Consensus 241 ~~C~aCgt~rp~~~~~~~~W~C~~Ct~~N~ 270 (299)
..|..|+..... ......|.|+.|++...
T Consensus 29 q~C~~CG~~~~~-~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 29 QTCPRCGHRNKK-RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred cCccCccccccc-ccccceEEcCCCCCEEC
Confidence 346666544333 12345788888887644
No 127
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=37.72 E-value=24 Score=32.50 Aligned_cols=22 Identities=27% Similarity=0.175 Sum_probs=17.9
Q ss_pred CHHHHHHHHHHHhhhcCCCCCC
Q 022290 47 PYEQILDTMLHELCHNEYGPHN 68 (299)
Q Consensus 47 p~~~i~~v~lHELaH~~~~~H~ 68 (299)
+.+.-..||+|||-|.+-..+.
T Consensus 68 ~~~r~rFtlAHELGH~llH~~~ 89 (213)
T COG2856 68 SLERKRFTLAHELGHALLHTDL 89 (213)
T ss_pred CHHHHHHHHHHHHhHHHhcccc
Confidence 5677889999999999865554
No 128
>PF14891 Peptidase_M91: Effector protein
Probab=37.38 E-value=11 Score=33.06 Aligned_cols=19 Identities=21% Similarity=0.132 Sum_probs=14.3
Q ss_pred HHHHHHHhhhcCCCCCChh
Q 022290 52 LDTMLHELCHNEYGPHNAD 70 (299)
Q Consensus 52 ~~v~lHELaH~~~~~H~~~ 70 (299)
.-+|.|||+|-.|.-++..
T Consensus 104 ~v~L~HEL~HA~~~~~Gt~ 122 (174)
T PF14891_consen 104 FVVLYHELIHAYDYMNGTM 122 (174)
T ss_pred HHHHHHHHHHHHHHHCCCC
Confidence 3678899999887666554
No 129
>PF15641 Tox-MPTase5: Metallopeptidase toxin 5
Probab=37.21 E-value=48 Score=26.81 Aligned_cols=39 Identities=18% Similarity=0.263 Sum_probs=28.0
Q ss_pred CCCCCCHHHHHHHHHHHhhhcC---------CC---CCChhHHHHHHHHHH
Q 022290 42 EWDFFPYEQILDTMLHELCHNE---------YG---PHNADFYKLWDEIRK 80 (299)
Q Consensus 42 ~~~f~p~~~i~~v~lHELaH~~---------~~---~H~~~F~~l~~~l~~ 80 (299)
...|.....+..|++||=-|-. |+ .-+++||..+++++.
T Consensus 55 ~~~f~sra~lr~~iiheelhhrw~~rgl~~hhp~gs~~~~~fy~~i~ry~~ 105 (109)
T PF15641_consen 55 FNSFSSRAELRNTIIHEELHHRWWKRGLNNHHPRGSEMSQRFYEIIRRYMS 105 (109)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHhhccccCCCCcchHHHHHHHHHHHHH
Confidence 3478888999999999866632 11 225789998887753
No 130
>PF12898 Stc1: Stc1 domain; InterPro: IPR024630 The domain contains 8 conserved cysteines that may bind to zinc. In S. pombe, proteins containing the domain act as protein linkers, which link the chromatin modifying CLRC complex to RNAi by tethering it to the RITS complex. This domain has a slightly different arrangement of its CxxC pairs from the LIM domain, hence it is not part of that family []. The tandem zinc-finger structure could mediate protein-protein interactions.
Probab=36.47 E-value=32 Score=26.93 Aligned_cols=28 Identities=25% Similarity=0.512 Sum_probs=20.0
Q ss_pred CCCcccCCcccccCCCCccccccCCCCCC
Q 022290 257 LKGWSCKFCTLDNSSLSERCLACGEWRYS 285 (299)
Q Consensus 257 ~~~W~C~~Ct~~N~~~~~~C~~Cg~~r~~ 285 (299)
...-.|..|+-. ...-.+|++|+..++-
T Consensus 35 ~~~i~C~~ct~~-q~~El~C~~C~~~k~l 62 (84)
T PF12898_consen 35 NSGIRCRECTGG-QVVELTCSPCGKTKPL 62 (84)
T ss_pred CCCCCCccCCCC-CcCcCEeccCCCCcCH
Confidence 456788888876 4445588889887764
No 131
>cd04327 ZnMc_MMP_like_3 Zinc-dependent metalloprotease; MMP_like sub-family 3. A group of bacterial and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=35.83 E-value=23 Score=31.41 Aligned_cols=19 Identities=26% Similarity=0.239 Sum_probs=15.4
Q ss_pred HHHHHHHHHhhhcCCCCCC
Q 022290 50 QILDTMLHELCHNEYGPHN 68 (299)
Q Consensus 50 ~i~~v~lHELaH~~~~~H~ 68 (299)
....|++|||-|.+-..|.
T Consensus 91 ~~~~~i~HElgHaLG~~HE 109 (198)
T cd04327 91 EFSRVVLHEFGHALGFIHE 109 (198)
T ss_pred hHHHHHHHHHHHHhcCccc
Confidence 4568999999999977664
No 132
>PHA02456 zinc metallopeptidase motif-containing protein
Probab=35.60 E-value=19 Score=30.36 Aligned_cols=15 Identities=40% Similarity=0.357 Sum_probs=12.4
Q ss_pred HHHHHHHHHhhhcCC
Q 022290 50 QILDTMLHELCHNEY 64 (299)
Q Consensus 50 ~i~~v~lHELaH~~~ 64 (299)
-.+.|+.|||+|+..
T Consensus 78 GC~~TL~HEL~H~WQ 92 (141)
T PHA02456 78 GCRDTLAHELNHAWQ 92 (141)
T ss_pred chHHHHHHHHHHHHh
Confidence 467999999999863
No 133
>PF07998 Peptidase_M54: Peptidase family M54; InterPro: IPR012962 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This entry represents zinc-dependent peptidases belonging to the MEROPS peptidase family M54, more commonly known as the archaemetzincins. The family has a wide taxonomic distribution, being found in archaea, bacteria and eukaryotes. Two human homologues have been characterised []. ; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding; PDB: 3LMC_A 2XHQ_A 2X7M_A.
Probab=35.47 E-value=25 Score=31.89 Aligned_cols=50 Identities=22% Similarity=0.226 Sum_probs=26.7
Q ss_pred CCccceecCCCcEEEEEecCC----CCCCCCCCHHHHHHHHHHHhhhcCCCCCChh
Q 022290 19 PSLLGINIGGGAEVKLRLRRP----NREWDFFPYEQILDTMLHELCHNEYGPHNAD 70 (299)
Q Consensus 19 ~~llGlN~n~G~~I~LrLR~~----~~~~~f~p~~~i~~v~lHELaH~~~~~H~~~ 70 (299)
.-+.|+-...|..--+.+-.+ .|.. +=.+.+..+++|||.|+.--+|=..
T Consensus 111 nfVFG~A~~~~~~aVvS~~~~~fy~~~~~--l~~~R~~Kea~HElGH~~GL~HC~~ 164 (194)
T PF07998_consen 111 NFVFGLARPGGGVAVVSTSRNEFYGEDEE--LFLERVCKEAVHELGHLFGLDHCEN 164 (194)
T ss_dssp SEBSEEEECCSSEEEEEGGCGGGGTSSHH--HHHHHHHHHHHHHHHHHTT----SS
T ss_pred ceEEEEeecCCCeEEEEEeccccccccHH--HHHHHHHHHHHHHHHHHcCCcCCCC
Confidence 446677666554333333211 0111 1147778999999999998888544
No 134
>PF05548 Peptidase_M11: Gametolysin peptidase M11; InterPro: IPR008752 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M11 (gametolysin family, clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH []. The type example is gametolysin from the unicellular biflagellated alga, Chlamydomonas reinhardtii Gametolysin is a zinc-containing metallo-protease, which is responsible for the degradation of the cell wall. Homologues of gametolysin have also been reported in the simple multicellular organism, Volvox [, ].
Probab=34.49 E-value=20 Score=34.70 Aligned_cols=43 Identities=23% Similarity=0.217 Sum_probs=26.9
Q ss_pred CccceecCCCcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCCCChh
Q 022290 20 SLLGINIGGGAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGPHNAD 70 (299)
Q Consensus 20 ~llGlN~n~G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~H~~~ 70 (299)
...|+-.-.|....+...... .... .|++|||-||.-..|+..
T Consensus 127 ~w~Gla~v~G~~~~~~~~~~~----~~~~----~~~~HElgHN~GL~Ha~~ 169 (314)
T PF05548_consen 127 GWAGLATVPGSQSWLWISGYG----VQDW----ATIMHELGHNLGLWHAGR 169 (314)
T ss_pred CceEEeecCCcceeeeecCcc----cccH----HHHHHHhhhhccccccCC
Confidence 345664334666666554321 1111 399999999999999964
No 135
>PRK09672 phage exclusion protein Lit; Provisional
Probab=33.81 E-value=22 Score=34.49 Aligned_cols=17 Identities=29% Similarity=0.505 Sum_probs=13.9
Q ss_pred HHHHHHHHHhhhcCCCC
Q 022290 50 QILDTMLHELCHNEYGP 66 (299)
Q Consensus 50 ~i~~v~lHELaH~~~~~ 66 (299)
.|-++++||++|+++..
T Consensus 164 A~a~i~~HEiaHv~~~h 180 (305)
T PRK09672 164 ALAWILLHEIAHVEFQH 180 (305)
T ss_pred HHHHHHHHHHHHHHhcc
Confidence 35689999999998764
No 136
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=33.46 E-value=29 Score=35.61 Aligned_cols=40 Identities=25% Similarity=0.541 Sum_probs=27.9
Q ss_pred CCCCccCCccc----cccccCCccccccCCCCCCCCCCCCCcccCCcccc
Q 022290 223 VGQMWQCNMCT----LLNQPLALTCEACGTQRNKSVGNLKGWSCKFCTLD 268 (299)
Q Consensus 223 ~~~~W~C~~CT----~~N~~~a~~C~aCgt~rp~~~~~~~~W~C~~Ct~~ 268 (299)
....-.|+.|. |.-....+.|.-|+...+. .|.|+.|.-.
T Consensus 219 Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~------~~~Cp~C~s~ 262 (505)
T TIGR00595 219 CGYILCCPNCDVSLTYHKKEGKLRCHYCGYQEPI------PKTCPQCGSE 262 (505)
T ss_pred CcCccCCCCCCCceEEecCCCeEEcCCCcCcCCC------CCCCCCCCCC
Confidence 33456788886 4455567789999876543 5889999754
No 137
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=33.41 E-value=22 Score=26.80 Aligned_cols=25 Identities=28% Similarity=0.510 Sum_probs=20.5
Q ss_pred cccCCcccccCCCCccccccCCCCC
Q 022290 260 WSCKFCTLDNSSLSERCLACGEWRY 284 (299)
Q Consensus 260 W~C~~Ct~~N~~~~~~C~~Cg~~r~ 284 (299)
-.|..|.++.+.....|..||....
T Consensus 5 kAC~~Ck~l~~~d~e~CP~Cgs~~~ 29 (64)
T COG2093 5 KACKNCKRLTPEDTEICPVCGSTDL 29 (64)
T ss_pred HHHhhccccCCCCCccCCCCCCccc
Confidence 4688898888888889999998754
No 138
>KOG3314 consensus Ku70-binding protein [Replication, recombination and repair]
Probab=33.22 E-value=47 Score=29.81 Aligned_cols=18 Identities=22% Similarity=0.318 Sum_probs=15.2
Q ss_pred CCHHHHHHHHHHHhhhcC
Q 022290 46 FPYEQILDTMLHELCHNE 63 (299)
Q Consensus 46 ~p~~~i~~v~lHELaH~~ 63 (299)
.-...+..||.|||.|..
T Consensus 86 ~~q~h~n~vv~HElIH~f 103 (194)
T KOG3314|consen 86 TIQDHVNQVVIHELIHAF 103 (194)
T ss_pred chHHHHHHHHHHHHHHHH
Confidence 455789999999999975
No 139
>KOG2760 consensus Vacuolar sorting protein VPS36 [Intracellular trafficking, secretion, and vesicular transport]
Probab=33.18 E-value=34 Score=34.51 Aligned_cols=47 Identities=19% Similarity=0.301 Sum_probs=32.1
Q ss_pred CCCCCccCCccccccccCC-ccccccCCCCC------CCCCCCCCcccCCcccc
Q 022290 222 DVGQMWQCNMCTLLNQPLA-LTCEACGTQRN------KSVGNLKGWSCKFCTLD 268 (299)
Q Consensus 222 ~~~~~W~C~~CT~~N~~~a-~~C~aCgt~rp------~~~~~~~~W~C~~Ct~~ 268 (299)
.....|.|+.|+++|-..- ..|..|+...- .+..+...--|+.|||.
T Consensus 86 ~~~~~~~~pls~vI~v~~~~~~~~~~g~~~~i~~~~~~~~~~~~~gp~~a~~~~ 139 (432)
T KOG2760|consen 86 DVEVTWVCPLSMVINVGEPAKSELTFGKINRIVVILHKPNPRFSPGPCPASTFA 139 (432)
T ss_pred ccceeeeeceeEEEEecCccchhhcccccceEEEEeCCCCCcCCCCCcccceee
Confidence 3446899999999997754 45888986532 22233356679999764
No 140
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=32.21 E-value=25 Score=28.24 Aligned_cols=29 Identities=24% Similarity=0.535 Sum_probs=18.7
Q ss_pred ccccccCCCCCCCCCCCCCcccCCcccccC
Q 022290 241 LTCEACGTQRNKSVGNLKGWSCKFCTLDNS 270 (299)
Q Consensus 241 ~~C~aCgt~rp~~~~~~~~W~C~~Ct~~N~ 270 (299)
..|..|+.+.-.. ...+.|.|..|.+.--
T Consensus 36 ~~Cp~C~~~~VkR-~a~GIW~C~kCg~~fA 64 (89)
T COG1997 36 HVCPFCGRTTVKR-IATGIWKCRKCGAKFA 64 (89)
T ss_pred CcCCCCCCcceee-eccCeEEcCCCCCeec
Confidence 3577777663222 3467899999986543
No 141
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=32.02 E-value=16 Score=37.78 Aligned_cols=54 Identities=22% Similarity=0.438 Sum_probs=34.8
Q ss_pred ccCCccccc---cccCCccccccCCCCCCC-----CCCCCCcccCCcccccCCCCccccccCC
Q 022290 227 WQCNMCTLL---NQPLALTCEACGTQRNKS-----VGNLKGWSCKFCTLDNSSLSERCLACGE 281 (299)
Q Consensus 227 W~C~~CT~~---N~~~a~~C~aCgt~rp~~-----~~~~~~W~C~~Ct~~N~~~~~~C~~Cg~ 281 (299)
=.|..|+-. |...-..|+.|...-.+. ..+++.|-|..|.+-- -....|++|-.
T Consensus 194 ~~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYGI~f~peG~WlCrkCi~~~-~~i~~C~fCps 255 (669)
T COG5141 194 DICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPEGFWLCRKCIYGE-YQIRCCSFCPS 255 (669)
T ss_pred hhhHhccccccCCcceEEEecCcchhhhhhcccceecCcchhhhhhhcccc-cceeEEEeccC
Confidence 456666543 333445688888654332 1567899999998743 34567999954
No 142
>COG3227 LasB Zinc metalloprotease (elastase) [Amino acid transport and metabolism]
Probab=30.20 E-value=13 Score=38.15 Aligned_cols=38 Identities=29% Similarity=0.419 Sum_probs=26.1
Q ss_pred ceecCC----CcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcC
Q 022290 23 GINIGG----GAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNE 63 (299)
Q Consensus 23 GlN~n~----G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~ 63 (299)
|.|+|. |..+.+ -+.|-..|-|+.--++|+.|||+|=+
T Consensus 308 G~~ynNAfWdG~qMvy---GDGDG~~f~~~S~sLDVvAHElTHGv 349 (507)
T COG3227 308 GKNYNNAFWDGDQMVY---GDGDGSFFTPFSGSLDVVAHELTHGV 349 (507)
T ss_pred ccccccccccCceeEe---ecCCcceecccccccceehhhhcchh
Confidence 555554 544433 24455678888888899999999955
No 143
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=29.44 E-value=13 Score=26.77 Aligned_cols=23 Identities=35% Similarity=0.729 Sum_probs=18.3
Q ss_pred ccCCccccccccCCccccccCCC
Q 022290 227 WQCNMCTLLNQPLALTCEACGTQ 249 (299)
Q Consensus 227 W~C~~CT~~N~~~a~~C~aCgt~ 249 (299)
=.|-.|.-.|+..+..|--|+..
T Consensus 15 kIC~rC~Arnp~~A~kCRkC~~k 37 (50)
T COG1552 15 KICRRCYARNPPRATKCRKCGYK 37 (50)
T ss_pred HHHHHhcCCCCcchhHHhhccCC
Confidence 46778888888888888888765
No 144
>PF10103 DUF2342: Uncharacterised conserved protein (DUF2342); InterPro: IPR018766 This entry represents a family of proteins whose function is currently unknown. These proteins are predominantly found in the actinobacteria (high GC Gram-positive bacteria), though some occur in other bacterial species and archaea. ; PDB: 3CMN_A.
Probab=29.25 E-value=33 Score=33.77 Aligned_cols=37 Identities=19% Similarity=-0.023 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHHhhhcCCCCCChhHHHHHHHHHHHH
Q 022290 46 FPYEQILDTMLHELCHNEYGPHNADFYKLWDEIRKEC 82 (299)
Q Consensus 46 ~p~~~i~~v~lHELaH~~~~~H~~~F~~l~~~l~~e~ 82 (299)
=|-+...|+.+||.||-+...|..---..+.....+|
T Consensus 152 ~~~d~rlwvalhE~aH~~lF~~~PWLr~~l~~~v~~~ 188 (342)
T PF10103_consen 152 DPDDFRLWVALHEAAHARLFAAVPWLRDHLLGAVEEY 188 (342)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHTSTHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHhhCchHHHHHHHHHHHH
Confidence 3556778999999999998888775555555555444
No 145
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=28.86 E-value=5.4 Score=28.94 Aligned_cols=41 Identities=27% Similarity=0.820 Sum_probs=27.1
Q ss_pred CccCCccccccccCC-ccccccCCCCCCCCCCCCCcccCCcccccCCCCccccccC
Q 022290 226 MWQCNMCTLLNQPLA-LTCEACGTQRNKSVGNLKGWSCKFCTLDNSSLSERCLACG 280 (299)
Q Consensus 226 ~W~C~~CT~~N~~~a-~~C~aCgt~rp~~~~~~~~W~C~~Ct~~N~~~~~~C~~Cg 280 (299)
..+|+.|.-.-+..- .+|+.|| .|.|..|...-. -.|..|+
T Consensus 7 ry~CDLCn~~~p~~~LRQCvlCG-----------RWaC~sCW~deY---Y~CksC~ 48 (57)
T PF14445_consen 7 RYSCDLCNSSHPISELRQCVLCG-----------RWACNSCWQDEY---YTCKSCN 48 (57)
T ss_pred hHhHHhhcccCcHHHHHHHhhhc-----------hhhhhhhhhhhH---hHHHhhh
Confidence 467777766655544 3588888 799999986543 3455554
No 146
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=28.75 E-value=23 Score=29.14 Aligned_cols=42 Identities=26% Similarity=0.589 Sum_probs=29.0
Q ss_pred cCCccc----cc-cccCCccccccCCCCCCCCCCCCCcccCCccccc-CCCCccccccCCC
Q 022290 228 QCNMCT----LL-NQPLALTCEACGTQRNKSVGNLKGWSCKFCTLDN-SSLSERCLACGEW 282 (299)
Q Consensus 228 ~C~~CT----~~-N~~~a~~C~aCgt~rp~~~~~~~~W~C~~Ct~~N-~~~~~~C~~Cg~~ 282 (299)
.|..|. |+ |.. ..|..|. ...|..|.... ....|.|.+|...
T Consensus 56 ~C~~C~~~fg~l~~~~--~~C~~C~-----------~~VC~~C~~~~~~~~~WlC~vC~k~ 103 (118)
T PF02318_consen 56 HCARCGKPFGFLFNRG--RVCVDCK-----------HRVCKKCGVYSKKEPIWLCKVCQKQ 103 (118)
T ss_dssp B-TTTS-BCSCTSTTC--EEETTTT-----------EEEETTSEEETSSSCCEEEHHHHHH
T ss_pred chhhhCCcccccCCCC--CcCCcCC-----------ccccCccCCcCCCCCCEEChhhHHH
Confidence 677773 22 333 5688887 67899999874 5678999998653
No 147
>COG3824 Predicted Zn-dependent protease [General function prediction only]
Probab=28.30 E-value=28 Score=29.67 Aligned_cols=15 Identities=27% Similarity=0.598 Sum_probs=12.2
Q ss_pred HHHHHHHHHHhhhcC
Q 022290 49 EQILDTMLHELCHNE 63 (299)
Q Consensus 49 ~~i~~v~lHELaH~~ 63 (299)
++|..|++||..|-.
T Consensus 107 d~vthvliHEIgHhF 121 (136)
T COG3824 107 DQVTHVLIHEIGHHF 121 (136)
T ss_pred hHhhhhhhhhhhhhc
Confidence 567889999999953
No 148
>PF13398 Peptidase_M50B: Peptidase M50B-like
Probab=27.70 E-value=34 Score=30.65 Aligned_cols=18 Identities=39% Similarity=0.746 Sum_probs=12.7
Q ss_pred CCHHHHHHHHHHHhhhcCC
Q 022290 46 FPYEQILDTMLHELCHNEY 64 (299)
Q Consensus 46 ~p~~~i~~v~lHELaH~~~ 64 (299)
+|+. +..|++||+.|.+-
T Consensus 18 ~~~~-~l~t~~HE~gHal~ 35 (200)
T PF13398_consen 18 YPFR-LLVTFVHELGHALA 35 (200)
T ss_pred HHHH-HHHHHHHHHHHHHH
Confidence 4444 44599999999653
No 149
>cd04283 ZnMc_hatching_enzyme Zinc-dependent metalloprotease, hatching enzyme-like subfamily. Hatching enzymes are secreted by teleost embryos to digest the egg envelope or chorion. In some teleosts, the hatching enzyme may be a system consisting of two evolutionary related metalloproteases, high choriolytic enzyme and low choriolytic enzyme (HCE and LCE), which may have different substrate specificities and cooperatively digest the chorion.
Probab=27.52 E-value=30 Score=30.96 Aligned_cols=16 Identities=31% Similarity=0.148 Sum_probs=13.3
Q ss_pred HHHHHHHhhhcCCCCC
Q 022290 52 LDTMLHELCHNEYGPH 67 (299)
Q Consensus 52 ~~v~lHELaH~~~~~H 67 (299)
..|++|||.|.+-.-|
T Consensus 78 ~G~i~HEl~HaLG~~H 93 (182)
T cd04283 78 KGIIQHELLHALGFYH 93 (182)
T ss_pred cchHHHHHHHHhCCcc
Confidence 4899999999986555
No 150
>PRK05580 primosome assembly protein PriA; Validated
Probab=27.19 E-value=45 Score=35.56 Aligned_cols=41 Identities=17% Similarity=0.525 Sum_probs=23.5
Q ss_pred ccccccCCCCCCCCCCCCCcccCCcccccCCCCccccccCCCC
Q 022290 241 LTCEACGTQRNKSVGNLKGWSCKFCTLDNSSLSERCLACGEWR 283 (299)
Q Consensus 241 ~~C~aCgt~rp~~~~~~~~W~C~~Ct~~N~~~~~~C~~Cg~~r 283 (299)
..|..|+.+-... .....-.|+.|++.-. -.+.|..|+...
T Consensus 391 ~~C~~C~~~l~~h-~~~~~l~Ch~Cg~~~~-~~~~Cp~Cg~~~ 431 (679)
T PRK05580 391 AECPHCDASLTLH-RFQRRLRCHHCGYQEP-IPKACPECGSTD 431 (679)
T ss_pred cCCCCCCCceeEE-CCCCeEECCCCcCCCC-CCCCCCCCcCCe
Confidence 3466665431110 2334567888887633 345788888764
No 151
>cd04276 ZnMc_MMP_like_2 Zinc-dependent metalloprotease; MMP_like sub-family 2. A group of bacterial metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=27.18 E-value=44 Score=30.21 Aligned_cols=20 Identities=25% Similarity=0.200 Sum_probs=17.7
Q ss_pred HHHHHHHHHHhhhcCCCCCC
Q 022290 49 EQILDTMLHELCHNEYGPHN 68 (299)
Q Consensus 49 ~~i~~v~lHELaH~~~~~H~ 68 (299)
+.+..+++||+-|.+--.|+
T Consensus 114 ~~~~~~~~he~gh~lGl~hn 133 (197)
T cd04276 114 ASLRYLLAHEVGHTLGLRHN 133 (197)
T ss_pred HHHHHHHHHHHHHHhcCccc
Confidence 56889999999999988885
No 152
>TIGR03624 putative hydrolase. Members of this protein family have a phylogenetic distribution skewed toward the Actinobacteria (high GC Gram-positive bacteria), but with a few members occuring in the Archaea and Chloroflexi. The function is unknown.
Probab=27.11 E-value=55 Score=32.33 Aligned_cols=37 Identities=19% Similarity=0.031 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHHhhhcCCCCCChhHHHHHHHHHHHH
Q 022290 46 FPYEQILDTMLHELCHNEYGPHNADFYKLWDEIRKEC 82 (299)
Q Consensus 46 ~p~~~i~~v~lHELaH~~~~~H~~~F~~l~~~l~~e~ 82 (299)
-|-+...|+.+||.||-....|..---..+.....+|
T Consensus 151 ~~~d~rlwlalhE~aH~~lF~avPWLr~~l~~~ve~~ 187 (345)
T TIGR03624 151 PPDDFRLWVALHEVTHRRQFRAVPWLRDHLEGAVEEL 187 (345)
T ss_pred CHHHHHHHHHHHHHHHHHHHhhCchHHHHHHHHHHHH
Confidence 4556778999999999998888875544444444443
No 153
>TIGR03883 DUF2342_F420 uncharacterized protein, coenzyme F420 biosynthesis associated. protein whose crystal structure has been determined (PDB:3CMN_A). This has been annotated as a putative hydrolase, but the support for that assertion is untraceable. There is no cofactor present in the structure.
Probab=27.07 E-value=58 Score=32.20 Aligned_cols=37 Identities=16% Similarity=-0.017 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHHhhhcCCCCCChhHHHHHHHHHHHH
Q 022290 46 FPYEQILDTMLHELCHNEYGPHNADFYKLWDEIRKEC 82 (299)
Q Consensus 46 ~p~~~i~~v~lHELaH~~~~~H~~~F~~l~~~l~~e~ 82 (299)
-|.+...|+.+||.||-....|..---..+.....+|
T Consensus 155 ~~~d~rlwlalhE~aH~~~F~avPWLr~~l~~~ve~~ 191 (346)
T TIGR03883 155 DPHDFRLWVCLHEVTHRVQFTAAPWLRDHLEGELEAL 191 (346)
T ss_pred CHHHHHHHHHHHHHHHHHHHhhCchHHHHHHHHHHHH
Confidence 4556778999999999999988875544444444443
No 154
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=26.64 E-value=50 Score=32.12 Aligned_cols=29 Identities=14% Similarity=0.235 Sum_probs=18.8
Q ss_pred HHHhhhcCCCCCChhHHHHHHHHHHHHHHHHH
Q 022290 56 LHELCHNEYGPHNADFYKLWDEIRKECDELMA 87 (299)
Q Consensus 56 lHELaH~~~~~H~~~F~~l~~~l~~e~~~l~~ 87 (299)
+-+||. ++--..|-.++.+|..-...+..
T Consensus 41 l~~LA~---~~pl~dYL~f~A~i~~aQ~~~l~ 69 (309)
T PRK03564 41 LRQLAE---NNPLGDYLRFAALIAEAQEVVLY 69 (309)
T ss_pred HHHHHh---cCChHHHHHHHHHHHHHHHHHHH
Confidence 345553 34456888888888877665543
No 155
>KOG1047 consensus Bifunctional leukotriene A4 hydrolase/aminopeptidase LTA4H [Lipid transport and metabolism; Posttranslational modification, protein turnover, chaperones; Defense mechanisms; Amino acid transport and metabolism]
Probab=26.64 E-value=32 Score=36.17 Aligned_cols=18 Identities=28% Similarity=0.566 Sum_probs=15.2
Q ss_pred HHHHHHHHHHhhhcCCCC
Q 022290 49 EQILDTMLHELCHNEYGP 66 (299)
Q Consensus 49 ~~i~~v~lHELaH~~~~~ 66 (299)
..+..||+||+||-..||
T Consensus 286 rsl~~vIaHEIAHSWtGN 303 (613)
T KOG1047|consen 286 RSLVDVIAHEIAHSWTGN 303 (613)
T ss_pred cchhhHHHHHhhhhhccc
Confidence 446799999999988886
No 156
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=26.37 E-value=31 Score=37.21 Aligned_cols=27 Identities=22% Similarity=0.560 Sum_probs=23.2
Q ss_pred CCCCCcccCCcccccCCCCccccccCC
Q 022290 255 GNLKGWSCKFCTLDNSSLSERCLACGE 281 (299)
Q Consensus 255 ~~~~~W~C~~Ct~~N~~~~~~C~~Cg~ 281 (299)
.+.+.|.|..|+-.--....+|+.|=.
T Consensus 44 VPtGpWfCrKCesqeraarvrCeLCP~ 70 (900)
T KOG0956|consen 44 VPTGPWFCRKCESQERAARVRCELCPH 70 (900)
T ss_pred cCCCchhhhhhhhhhhhccceeecccC
Confidence 467889999999988888899999943
No 157
>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]
Probab=26.36 E-value=37 Score=34.99 Aligned_cols=35 Identities=14% Similarity=0.040 Sum_probs=24.0
Q ss_pred CcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCCC
Q 022290 29 GAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYGP 66 (299)
Q Consensus 29 G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~~ 66 (299)
|..|-|+--+-- .--....|..||.||+.|+..++
T Consensus 111 Gg~v~vntGLll---~ae~esElagViAHEigHv~qrH 145 (484)
T COG4783 111 GGYVVVNTGLLL---TAENESELAGVIAHEIGHVAQRH 145 (484)
T ss_pred CceEEEehHHHH---hcCCHHHHHHHHHHHHHHHhhhh
Confidence 667777754311 12345789999999999998653
No 158
>cd04281 ZnMc_BMP1_TLD Zinc-dependent metalloprotease; BMP1/TLD-like subfamily. BMP1 (Bone morphogenetic protein 1) and TLD (tolloid)-like metalloproteases play vital roles in extracellular matrix formation, by cleaving precursor proteins such as enzymes, structural proteins, and proteins involved in the mineralization of the extracellular matrix. The drosophila protein tolloid and its Xenopus homologue xolloid cleave and inactivate Sog and chordin, respectively, which are inhibitors of Dpp (the Drosophila decapentaplegic gene product) and its homologue BMP4, involved in dorso-ventral patterning.
Probab=26.32 E-value=31 Score=31.29 Aligned_cols=17 Identities=29% Similarity=0.204 Sum_probs=13.9
Q ss_pred HHHHHHHhhhcCCCCCC
Q 022290 52 LDTMLHELCHNEYGPHN 68 (299)
Q Consensus 52 ~~v~lHELaH~~~~~H~ 68 (299)
..|++|||.|-+-.-|.
T Consensus 88 ~Gti~HEl~HaLGf~HE 104 (200)
T cd04281 88 FGIVVHELGHVIGFWHE 104 (200)
T ss_pred CchHHHHHHHHhcCcch
Confidence 48999999999866654
No 159
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=26.28 E-value=48 Score=24.27 Aligned_cols=31 Identities=23% Similarity=0.523 Sum_probs=23.1
Q ss_pred ccccCCccccccCCCCCCCCCCCCCcccCCcccccCC
Q 022290 235 LNQPLALTCEACGTQRNKSVGNLKGWSCKFCTLDNSS 271 (299)
Q Consensus 235 ~N~~~a~~C~aCgt~rp~~~~~~~~W~C~~Ct~~N~~ 271 (299)
++.+....|..||..+.. .-.|..|+|.+.-
T Consensus 22 l~~~~l~~C~~CG~~~~~------H~vC~~CG~Y~gr 52 (57)
T PRK12286 22 LKAPGLVECPNCGEPKLP------HRVCPSCGYYKGR 52 (57)
T ss_pred ccCCcceECCCCCCccCC------eEECCCCCcCCCE
Confidence 466677789999987654 5788899887653
No 160
>PRK14873 primosome assembly protein PriA; Provisional
Probab=26.16 E-value=45 Score=35.66 Aligned_cols=22 Identities=36% Similarity=0.840 Sum_probs=10.9
Q ss_pred cccCCcc----cccCCCCccccccCC
Q 022290 260 WSCKFCT----LDNSSLSERCLACGE 281 (299)
Q Consensus 260 W~C~~Ct----~~N~~~~~~C~~Cg~ 281 (299)
-.|+.|. |+.......|.-||.
T Consensus 393 ~~C~~C~~~L~~h~~~~~l~Ch~CG~ 418 (665)
T PRK14873 393 ARCRHCTGPLGLPSAGGTPRCRWCGR 418 (665)
T ss_pred eECCCCCCceeEecCCCeeECCCCcC
Confidence 4566665 222233455666665
No 161
>KOG0593 consensus Predicted protein kinase KKIAMRE [General function prediction only]
Probab=26.06 E-value=51 Score=32.71 Aligned_cols=37 Identities=24% Similarity=0.202 Sum_probs=27.7
Q ss_pred CCCHHHHHHHHHHHhhhcCCCCCChhHHHHHHHHHHH
Q 022290 45 FFPYEQILDTMLHELCHNEYGPHNADFYKLWDEIRKE 81 (299)
Q Consensus 45 f~p~~~i~~v~lHELaH~~~~~H~~~F~~l~~~l~~e 81 (299)
.+=||.++.||||||-|+-+|=-+..-.+++-|+...
T Consensus 77 hLVFE~~dhTvL~eLe~~p~G~~~~~vk~~l~Q~l~a 113 (396)
T KOG0593|consen 77 HLVFEYCDHTVLHELERYPNGVPSELVKKYLYQLLKA 113 (396)
T ss_pred EEEeeecchHHHHHHHhccCCCCHHHHHHHHHHHHHH
Confidence 3455679999999999999987776666666555543
No 162
>PF14247 DUF4344: Domain of unknown function (DUF4344)
Probab=25.78 E-value=46 Score=30.80 Aligned_cols=21 Identities=29% Similarity=0.320 Sum_probs=15.9
Q ss_pred HHHHHHHHHHhhhcCCCCCCh
Q 022290 49 EQILDTMLHELCHNEYGPHNA 69 (299)
Q Consensus 49 ~~i~~v~lHELaH~~~~~H~~ 69 (299)
..+..|++||+.|.+....+-
T Consensus 90 ~~~~~~l~HE~GHAlI~~~~l 110 (220)
T PF14247_consen 90 GNVLFTLYHELGHALIDDLDL 110 (220)
T ss_pred HHHHHHHHHHHHHHHHHHhcC
Confidence 456789999999987765543
No 163
>PF15640 Tox-MPTase4: Metallopeptidase toxin 4
Probab=25.49 E-value=64 Score=27.62 Aligned_cols=49 Identities=33% Similarity=0.429 Sum_probs=30.2
Q ss_pred CCCCccEeeeecc--cCCCCCCccceecCCCcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcC
Q 022290 1 MRKHKWKVRILSE--FCPANPSLLGINIGGGAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNE 63 (299)
Q Consensus 1 Mr~~~w~V~~L~E--~~P~~~~llGlN~n~G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~ 63 (299)
|.+.|-+|.+=.- .+|.+.. -|.|.--|+ |.||=+.. .+-|+||--|-.
T Consensus 31 m~~~gIkV~Idkk~kilP~n~a-agFd~~tg~-I~lr~~pt------------~~~~~HE~~Ha~ 81 (132)
T PF15640_consen 31 MGKRGIKVKIDKKDKILPENKA-AGFDPETGE-IYLRKNPT------------LISALHESYHAK 81 (132)
T ss_pred HHhCCcEEEECCccCCCCcccc-ccCCCCCCc-EEEcCCch------------HHHHHHHHHHHH
Confidence 4456666654433 4564433 366666674 77776552 378999988864
No 164
>PRK12496 hypothetical protein; Provisional
Probab=25.47 E-value=41 Score=29.53 Aligned_cols=10 Identities=40% Similarity=0.414 Sum_probs=5.8
Q ss_pred HHHHHHHHHH
Q 022290 154 IQAAAMAAER 163 (299)
Q Consensus 154 re~~a~AAer 163 (299)
.+++|.|.+-
T Consensus 81 ~~~iaLA~el 90 (164)
T PRK12496 81 IEVLALALEL 90 (164)
T ss_pred HHHHHHHHHh
Confidence 3566666654
No 165
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=25.13 E-value=37 Score=24.83 Aligned_cols=40 Identities=20% Similarity=0.415 Sum_probs=21.1
Q ss_pred ccccccCCCCCCCCCCCCCcccCCcccccCCC----Cccccc--cCCCC
Q 022290 241 LTCEACGTQRNKSVGNLKGWSCKFCTLDNSSL----SERCLA--CGEWR 283 (299)
Q Consensus 241 ~~C~aCgt~rp~~~~~~~~W~C~~Ct~~N~~~----~~~C~~--Cg~~r 283 (299)
..|..|+.+-- .....-.|+.|+..-+.. ...|.. |+++.
T Consensus 6 ~~C~~Cg~~~~---~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~ 51 (54)
T PF14446_consen 6 CKCPVCGKKFK---DGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF 51 (54)
T ss_pred ccChhhCCccc---CCCCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence 35777775421 123356777777554433 345655 65544
No 166
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=24.44 E-value=53 Score=31.90 Aligned_cols=41 Identities=15% Similarity=0.254 Sum_probs=25.0
Q ss_pred CHHHHHHHHHHHhhhcCCCCCChhHHHHHHHHHHHHHHHHH
Q 022290 47 PYEQILDTMLHELCHNEYGPHNADFYKLWDEIRKECDELMA 87 (299)
Q Consensus 47 p~~~i~~v~lHELaH~~~~~H~~~F~~l~~~l~~e~~~l~~ 87 (299)
+...+-..=..=|-++-..+.-..|-.++.++..-..++..
T Consensus 25 ~~~~lf~~RA~RL~~LA~~~pl~dyL~f~A~la~aQ~~~l~ 65 (305)
T TIGR01562 25 PLRDLFNRRAERLLQLAEGHPLGDYLRFVAGICRLQQALLD 65 (305)
T ss_pred ChhhHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHh
Confidence 33334333344444555555558999999988877766544
No 167
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=24.41 E-value=44 Score=31.46 Aligned_cols=28 Identities=18% Similarity=0.528 Sum_probs=23.3
Q ss_pred CCCCCccCCccccccccCCccccccCCC
Q 022290 222 DVGQMWQCNMCTLLNQPLALTCEACGTQ 249 (299)
Q Consensus 222 ~~~~~W~C~~CT~~N~~~a~~C~aCgt~ 249 (299)
..+..|.|..|.+.=......|..|++-
T Consensus 350 ~~~p~~~c~~cg~~~~~~~~~c~~c~~~ 377 (389)
T PRK11788 350 KRKPRYRCRNCGFTARTLYWHCPSCKAW 377 (389)
T ss_pred hCCCCEECCCCCCCCccceeECcCCCCc
Confidence 3445699999999999999999999864
No 168
>cd06158 S2P-M50_like_1 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group includes bacterial, eukaryotic, and Archaeal S2P/M50s homologs with a minimal core protein and no PDZ domains.
Probab=24.28 E-value=47 Score=29.41 Aligned_cols=14 Identities=36% Similarity=0.546 Sum_probs=11.4
Q ss_pred HHHHHHHHHhhhcC
Q 022290 50 QILDTMLHELCHNE 63 (299)
Q Consensus 50 ~i~~v~lHELaH~~ 63 (299)
.+..+++||++|-.
T Consensus 8 ~~~~i~~HE~aHa~ 21 (181)
T cd06158 8 VLLAITLHEFAHAY 21 (181)
T ss_pred HHHHHHHHHHHHHH
Confidence 56789999999854
No 169
>PF02163 Peptidase_M50: Peptidase family M50; InterPro: IPR008915 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This entry contains metallopeptidases belonging to MEROPS peptidase family M50 (S2P protease family, clan MM). Members of the M50 metallopeptidase family include: mammalian sterol-regulatory element binding protein (SREBP) site 2 protease, Escherichia coli protease EcfE, stage IV sporulation protein FB and various hypothetical bacterial and eukaryotic homologues. A number of proteins are classified as non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity.; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 3B4R_A 3ID4_A 3ID2_A 2ZPL_B 3ID1_A 2ZPM_A 3ID3_B 2HGA_A.
Probab=24.26 E-value=47 Score=28.77 Aligned_cols=14 Identities=36% Similarity=0.572 Sum_probs=11.6
Q ss_pred HHHHHHHHHhhhcC
Q 022290 50 QILDTMLHELCHNE 63 (299)
Q Consensus 50 ~i~~v~lHELaH~~ 63 (299)
.+..+++||+.|..
T Consensus 6 ~~i~i~~HE~gH~~ 19 (192)
T PF02163_consen 6 LLISIVLHELGHAL 19 (192)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred cccccccccccccc
Confidence 46688999999975
No 170
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=24.25 E-value=29 Score=23.42 Aligned_cols=27 Identities=22% Similarity=0.432 Sum_probs=12.0
Q ss_pred cccccCCCCCCCCCCCCCcccCCcccc
Q 022290 242 TCEACGTQRNKSVGNLKGWSCKFCTLD 268 (299)
Q Consensus 242 ~C~aCgt~rp~~~~~~~~W~C~~Ct~~ 268 (299)
+|..|+..........+...|..|+++
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-BB
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCCE
Confidence 355555443111233445566666643
No 171
>cd04282 ZnMc_meprin Zinc-dependent metalloprotease, meprin_like subfamily. Meprins are membrane-bound or secreted extracellular proteases, which cleave a variety of targets, including peptides such as parathyroid hormone, gastrin, and cholecystokinin, cytokines such as osteopontin, and proteins such as collagen IV, fibronectin, casein and gelatin. Meprins may also be able to release proteins from the cell surface. Closely related meprin alpha- and beta-subunits form homo- and hetero-oligomers; these complexes are found on epithelial cells of the intestine, for example, and are also expressed in certain cancer cells.
Probab=24.18 E-value=34 Score=31.80 Aligned_cols=17 Identities=29% Similarity=0.129 Sum_probs=13.6
Q ss_pred HHHHHHHhhhcCCCCCC
Q 022290 52 LDTMLHELCHNEYGPHN 68 (299)
Q Consensus 52 ~~v~lHELaH~~~~~H~ 68 (299)
..|++|||.|-+-.-|-
T Consensus 121 ~Gti~HEl~HalGf~HE 137 (230)
T cd04282 121 KATVEHEFLHALGFYHE 137 (230)
T ss_pred CchHHHHHHHHhCCccc
Confidence 48999999999865543
No 172
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=23.09 E-value=49 Score=25.01 Aligned_cols=21 Identities=24% Similarity=0.499 Sum_probs=13.7
Q ss_pred cccCCcccccCCCCccccccCCC
Q 022290 260 WSCKFCTLDNSSLSERCLACGEW 282 (299)
Q Consensus 260 W~C~~Ct~~N~~~~~~C~~Cg~~ 282 (299)
-.|..|-+.++ ...|..||..
T Consensus 6 ~AC~~C~~i~~--~~~Cp~Cgs~ 26 (64)
T PRK06393 6 RACKKCKRLTP--EKTCPVHGDE 26 (64)
T ss_pred hhHhhCCcccC--CCcCCCCCCC
Confidence 45777777774 3377777764
No 173
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=22.97 E-value=84 Score=34.41 Aligned_cols=60 Identities=22% Similarity=0.462 Sum_probs=44.8
Q ss_pred CCccCCccccccccCCccccccCCCCCCCC------CCCCCcccCCcccccC----CCCccccccCCCCC
Q 022290 225 QMWQCNMCTLLNQPLALTCEACGTQRNKSV------GNLKGWSCKFCTLDNS----SLSERCLACGEWRY 284 (299)
Q Consensus 225 ~~W~C~~CT~~N~~~a~~C~aCgt~rp~~~------~~~~~W~C~~Ct~~N~----~~~~~C~~Cg~~r~ 284 (299)
..=.|.+|...=+++.+.|.-|.+.-|.=+ .....|-|+.|----. ++-..|..|..+-.
T Consensus 1116 ~~vdc~~cg~~i~~~~~~c~ec~~kfP~CiasG~pIt~~~fWlC~~CkH~a~~~EIs~y~~CPLCHs~~~ 1185 (1189)
T KOG2041|consen 1116 AKVDCSVCGAKIDPYDLQCSECQTKFPVCIASGRPITDNIFWLCPRCKHRAHQHEISKYNCCPLCHSMES 1185 (1189)
T ss_pred cceeeeecCCcCCccCCCChhhcCcCceeeccCCccccceEEEccccccccccccccccccCccccChhh
Confidence 467899999999999999999988766422 3455899999974332 44678999987653
No 174
>PF08434 CLCA_N: Calcium-activated chloride channel; InterPro: IPR013642 The CLCA family of calcium-activated chloride channels has been identified in many epithelial and endothelial cell types as well as in smooth muscle cells [] and has four or five putative transmembrane regions. Additionally to their role as chloride channels some CLCA proteins function as adhesion molecules and may also have roles as tumour suppressors []. The domain described here is found at the N terminus of CLCAs.
Probab=22.84 E-value=19 Score=34.28 Aligned_cols=38 Identities=18% Similarity=0.162 Sum_probs=22.4
Q ss_pred ecCCCcEEEEEecCCCCC--CCCCCHHHHHHHHHHHhhhcCCC
Q 022290 25 NIGGGAEVKLRLRRPNRE--WDFFPYEQILDTMLHELCHNEYG 65 (299)
Q Consensus 25 N~n~G~~I~LrLR~~~~~--~~f~p~~~i~~v~lHELaH~~~~ 65 (299)
+-..|+.|.|--..-.++ ..|-| .-.+|+||-||+.+|
T Consensus 124 CGe~G~yIhltp~fl~~~~~~~yG~---~grv~VhEWAhlRWG 163 (262)
T PF08434_consen 124 CGEPGEYIHLTPDFLLGDNLSQYGP---RGRVFVHEWAHLRWG 163 (262)
T ss_pred CCCCCeeEEechhhhcCCchhhcCC---cceeeeehhhhhccc
Confidence 444577777732221111 12222 357899999999987
No 175
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=22.43 E-value=40 Score=35.96 Aligned_cols=17 Identities=53% Similarity=1.367 Sum_probs=12.6
Q ss_pred CCccCCccccccccCCccccccCCC
Q 022290 225 QMWQCNMCTLLNQPLALTCEACGTQ 249 (299)
Q Consensus 225 ~~W~C~~CT~~N~~~a~~C~aCgt~ 249 (299)
..|.|+-|+ .|++|++.
T Consensus 61 ~gWrC~~cr--------vCe~c~~~ 77 (694)
T KOG4443|consen 61 GGWRCPSCR--------VCEACGTT 77 (694)
T ss_pred CCcccCCce--------eeeecccc
Confidence 459999996 57777743
No 176
>cd04280 ZnMc_astacin_like Zinc-dependent metalloprotease, astacin_like subfamily or peptidase family M12A, a group of zinc-dependent proteolytic enzymes with a HExxH zinc-binding site/active site. Members of this family may have an amino terminal propeptide, which is cleaved to yield the active protease domain, which is consequently always found at the N-terminus in multi-domain architectures. This family includes: astacin, a digestive enzyme from Crayfish; meprin, a multiple domain membrane component that is constructed from a homologous alpha and beta chain, proteins involved in (bone) morphogenesis, tolloid from drosophila, and the sea urchin SPAN protein, which may also play a role in development.
Probab=22.39 E-value=39 Score=29.69 Aligned_cols=17 Identities=41% Similarity=0.415 Sum_probs=13.8
Q ss_pred HHHHHHHhhhcCCCCCC
Q 022290 52 LDTMLHELCHNEYGPHN 68 (299)
Q Consensus 52 ~~v~lHELaH~~~~~H~ 68 (299)
..|++|||.|-+-..|.
T Consensus 75 ~g~v~HE~~HalG~~HE 91 (180)
T cd04280 75 LGTIVHELMHALGFYHE 91 (180)
T ss_pred CchhHHHHHHHhcCcch
Confidence 58999999999866553
No 177
>cd06162 S2P-M50_PDZ_SREBP Sterol regulatory element-binding protein (SREBP) Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50A), regulates intramembrane proteolysis (RIP) of SREBP and is part of a signal transduction mechanism involved in sterol and lipid metabolism. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of SREBPs from membranes of the endoplasmic reticulum (ER). These domains translocate into the nucleus, where they activate genes of cholesterol and fatty acid biosynthesis. The first cleavage occurs at Site-1 within the ER lumen to generate an intermediate that is subsequently released from the membrane by cleavage at Site-2, which lies within the first transmembrane domain. It is the second proteolytic step that is carried out by the SREBP Site-2 protease (S2P) which is present in this CD family. This group appears to be limited to eumetazoan proteins and contains one PDZ domain.
Probab=22.38 E-value=52 Score=31.53 Aligned_cols=14 Identities=21% Similarity=0.518 Sum_probs=11.2
Q ss_pred HHHHHHHHHhhhcC
Q 022290 50 QILDTMLHELCHNE 63 (299)
Q Consensus 50 ~i~~v~lHELaH~~ 63 (299)
.+..+++|||+|-+
T Consensus 134 l~isvvvHElgHal 147 (277)
T cd06162 134 LLISGVVHEMGHGV 147 (277)
T ss_pred HHHHHHHHHHHHHH
Confidence 35678899999965
No 178
>PRK04023 DNA polymerase II large subunit; Validated
Probab=22.34 E-value=70 Score=36.01 Aligned_cols=47 Identities=23% Similarity=0.381 Sum_probs=35.8
Q ss_pred ccccccccCCccccccCCCCCCCCCCCCCcccCCcccccCCCCccccccCCCCCC
Q 022290 231 MCTLLNQPLALTCEACGTQRNKSVGNLKGWSCKFCTLDNSSLSERCLACGEWRYS 285 (299)
Q Consensus 231 ~CT~~N~~~a~~C~aCgt~rp~~~~~~~~W~C~~Ct~~N~~~~~~C~~Cg~~r~~ 285 (299)
.=++.++.....|..|+..- ....|+.|+... .....|.-|++.-..
T Consensus 617 ~g~~eVEVg~RfCpsCG~~t-------~~frCP~CG~~T-e~i~fCP~CG~~~~~ 663 (1121)
T PRK04023 617 KGTIEVEIGRRKCPSCGKET-------FYRRCPFCGTHT-EPVYRCPRCGIEVEE 663 (1121)
T ss_pred CCceeecccCccCCCCCCcC-------CcccCCCCCCCC-CcceeCccccCcCCC
Confidence 34566788888999999773 357899999884 556699999876543
No 179
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=21.89 E-value=72 Score=21.80 Aligned_cols=31 Identities=19% Similarity=0.528 Sum_probs=17.2
Q ss_pred cccccCCCCCCCCC-CCCCcccCCcccccCCC
Q 022290 242 TCEACGTQRNKSVG-NLKGWSCKFCTLDNSSL 272 (299)
Q Consensus 242 ~C~aCgt~rp~~~~-~~~~W~C~~Ct~~N~~~ 272 (299)
.|..|+..-..... ....|.|+.|.|.....
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~~ 33 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEPIE 33 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeEECC
Confidence 46677654322211 11368888888765544
No 180
>PF01400 Astacin: Astacin (Peptidase family M12A) This Prosite motif covers only the active site.; InterPro: IPR001506 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M12, subfamily M12A (astacin family, clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH []. The astacin () family of metalloendopeptidases encompasses a range of proteins found in hydra to humans, in mature and developmental systems []. Their functions include activation of growth factors, degradation of polypeptides, and processing of extracellular proteins []. The proteins are synthesised with N-terminal signal and pro-enzyme sequences, and many contain multiple domains C-terminal to the protease domain. They are either secreted from cells, or are associated with the plasma membrane. The astacin molecule adopts a kidney shape, with a deep active-site cleft between its N- and C-terminal domains []. The zinc ion, which lies at the bottom of the cleft, exhibits a unique penta-coordinated mode of binding, involving 3 histidine residues, a tyrosine and a water molecule (which is also bound to the carboxylate side chain of Glu93) []. The N-terminal domain comprises 2 alpha-helices and a 5-stranded beta-sheet. The overall topology of this domain is shared by the archetypal zinc-endopeptidase thermolysin. Astacin protease domains also share common features with serralysins, matrix metalloendopeptidases, and snake venom proteases; they cleave peptide bonds in polypeptides such as insulin B chain and bradykinin, and in proteins such as casein and gelatin; and they have arylamidase activity [].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 3LQB_A 3EDH_A 3EDG_A 3EDI_A 1IAE_A 1IAB_A 1IAA_A 1AST_A 1IAC_A 1QJJ_A ....
Probab=21.84 E-value=39 Score=30.03 Aligned_cols=17 Identities=41% Similarity=0.356 Sum_probs=12.2
Q ss_pred HHHHHHHhhhcCCCCCC
Q 022290 52 LDTMLHELCHNEYGPHN 68 (299)
Q Consensus 52 ~~v~lHELaH~~~~~H~ 68 (299)
..|++|||.|-+-..|-
T Consensus 80 ~~~i~HEl~HaLG~~HE 96 (191)
T PF01400_consen 80 VGTILHELGHALGFWHE 96 (191)
T ss_dssp HHHHHHHHHHHHTB--G
T ss_pred ccchHHHHHHHHhhhhh
Confidence 46999999998865553
No 181
>cd06258 Peptidase_M3_like The peptidase M3-like family, also called neurolysin-like family, is part of the "zincins" metallopeptidases, and includes M3, M2 and M32 families of metallopeptidases. The M3 family is subdivided into two subfamilies: the widespread M3A, which comprises a number of high-molecular mass endo- and exopeptidases from bacteria, archaea, protozoa, fungi, plants and animals, and the small M3B, whose members are enzymes primarily from bacteria. Well-known mammalian/eukaryotic M3A endopeptidases are the thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (alias endopeptidase 3.4.24.16), and the mitochondrial intermediate peptidase. The first two are intracellular oligopeptidases, which act only on relatively short substrates of less than 20 amino acid residues, while the latter cleaves N-terminal octapeptides from proteins during their import into the mitochondria. The M3A subfamily also contains several bacterial endopeptidases, collectively called olig
Probab=21.72 E-value=70 Score=30.71 Aligned_cols=50 Identities=18% Similarity=0.246 Sum_probs=27.6
Q ss_pred EEEEecCCCCCC-CCCCHHHHHHHHHHHhhhcCCC-------C------CChhHHHHHHHHHHHH
Q 022290 32 VKLRLRRPNREW-DFFPYEQILDTMLHELCHNEYG-------P------HNADFYKLWDEIRKEC 82 (299)
Q Consensus 32 I~LrLR~~~~~~-~f~p~~~i~~v~lHELaH~~~~-------~------H~~~F~~l~~~l~~e~ 82 (299)
|..|+..+.+.. ..+.+..| .||+||+-|.+|. . -+..|.+...+++..+
T Consensus 135 i~~n~~~~~~~~~~ll~~~~v-~tl~HE~GHa~h~~l~~~~~~~~~g~~~~~~~~E~~S~~~E~~ 198 (365)
T cd06258 135 ILANFTSPAAPDPVLLGHDDI-NTLFHEFGHAVHFLLIQQRYPFQERTPTSTDFAEAQSMFLESF 198 (365)
T ss_pred EEccCCCCCCCCCCcCCHHHH-HHHHHHHhHHHHHHHhcCCCCcCCCCCCCccHHhccHHHHHHH
Confidence 444444432221 33444544 6899999887754 1 2345666666666544
No 182
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=21.49 E-value=69 Score=26.28 Aligned_cols=24 Identities=25% Similarity=0.607 Sum_probs=17.3
Q ss_pred CcccCCcc----cccCCCCccccccCCC
Q 022290 259 GWSCKFCT----LDNSSLSERCLACGEW 282 (299)
Q Consensus 259 ~W~C~~Ct----~~N~~~~~~C~~Cg~~ 282 (299)
.|.|..|+ ..|......|..|+..
T Consensus 42 ~~~C~~Cg~~~~~~~SCk~R~CP~C~~~ 69 (111)
T PF14319_consen 42 RYRCEDCGHEKIVYNSCKNRHCPSCQAK 69 (111)
T ss_pred eeecCCCCceEEecCcccCcCCCCCCCh
Confidence 57777777 4566777788888764
No 183
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=21.40 E-value=60 Score=24.27 Aligned_cols=21 Identities=29% Similarity=0.813 Sum_probs=11.8
Q ss_pred ccCCcccccCCCCccccccCCCC
Q 022290 261 SCKFCTLDNSSLSERCLACGEWR 283 (299)
Q Consensus 261 ~C~~Ct~~N~~~~~~C~~Cg~~r 283 (299)
.|..|-+.+... .|..||..-
T Consensus 5 AC~~C~~i~~~~--~CP~Cgs~~ 25 (61)
T PRK08351 5 ACRHCHYITTED--RCPVCGSRD 25 (61)
T ss_pred hhhhCCcccCCC--cCCCCcCCc
Confidence 466666666332 566666643
No 184
>KOG2719 consensus Metalloprotease [General function prediction only]
Probab=20.95 E-value=50 Score=33.60 Aligned_cols=45 Identities=18% Similarity=0.195 Sum_probs=29.9
Q ss_pred CCCccceecCCCcEEEEEecCCCCCCCCCCHHHHHHHHHHHhhhcCCC
Q 022290 18 NPSLLGINIGGGAEVKLRLRRPNREWDFFPYEQILDTMLHELCHNEYG 65 (299)
Q Consensus 18 ~~~llGlN~n~G~~I~LrLR~~~~~~~f~p~~~i~~v~lHELaH~~~~ 65 (299)
|+-+.|+..|+.-+|.=.|-.. .....-|+|..|+.|||.|-.++
T Consensus 250 NAyfyG~~~~KRIvIyDtLl~~---~~~~~~eel~AVl~HELGHW~~~ 294 (428)
T KOG2719|consen 250 NAYFYGLCKNKRIVIYDTLLLE---EEHLNNEELVAVLAHELGHWKLN 294 (428)
T ss_pred CeeeeeccccceEEEehhhhhh---hhccccHHHHHHHHHHhhHHHHh
Confidence 5667788777765553333320 11156689999999999997664
No 185
>cd05709 S2P-M50 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. The domain core structure appears to contain at least three transmembrane helices with a catalytic zinc atom coordinated by three conserved residues contained within the consensus sequence HExxH, together with a conserved aspartate residue. The S2P/M50 family of RIP proteases is widely distributed; in eukaryotic cells, they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum (ER) stress responses. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of sterol regulatory element-bindin
Probab=20.84 E-value=60 Score=27.96 Aligned_cols=14 Identities=29% Similarity=0.482 Sum_probs=11.7
Q ss_pred HHHHHHHHHhhhcC
Q 022290 50 QILDTMLHELCHNE 63 (299)
Q Consensus 50 ~i~~v~lHELaH~~ 63 (299)
.+..+++||+.|..
T Consensus 7 ~~i~i~iHE~gH~~ 20 (180)
T cd05709 7 LLISVTVHELGHAL 20 (180)
T ss_pred HHHHHHHHHHHHHH
Confidence 45678999999976
No 186
>cd06164 S2P-M50_SpoIVFB_CBS SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. In this subgroup, SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain. SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. It has been proposed tha
Probab=20.71 E-value=60 Score=29.82 Aligned_cols=14 Identities=36% Similarity=0.506 Sum_probs=11.1
Q ss_pred HHHHHHHHHhhhcC
Q 022290 50 QILDTMLHELCHNE 63 (299)
Q Consensus 50 ~i~~v~lHELaH~~ 63 (299)
...-+++|||.|..
T Consensus 52 l~~~v~iHElgH~~ 65 (227)
T cd06164 52 LFASVLLHELGHSL 65 (227)
T ss_pred HHHHHHHHHHHHHH
Confidence 34578899999965
No 187
>PF01432 Peptidase_M3: Peptidase family M3 This Prosite motif covers only the active site. This family belongs to family M3 of the peptidase classification.; InterPro: IPR001567 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M3 (clan MA(E)), subfamilies M3A and M3B. The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. The Thimet oligopeptidase family, is a large family of archaeal, bacterial and eukaryotic oligopeptidases that cleave medium sized peptides. The group contains: mitochondrial intermediate peptidase (3.4.24.59 from EC) Neurolysin, mitochondrial precursor, (3.4.24.16 from EC) Thimet oligopeptidase (3.4.24.15 from EC) Dipeptidyl carboxypeptidase (3.4.15.5 from EC) Oligopeptidase A (3.4.24.70 from EC) Oligoendopeptidase F ; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2QR4_B 3CE2_A 1Y79_1 2H1J_A 2H1N_A 2O36_A 1S4B_P 2O3E_A 1I1I_P.
Probab=20.26 E-value=84 Score=31.28 Aligned_cols=34 Identities=15% Similarity=0.308 Sum_probs=20.5
Q ss_pred EEEEEecCCC-CCCCCCCHHHHHHHHHHHhhhcCCC
Q 022290 31 EVKLRLRRPN-REWDFFPYEQILDTMLHELCHNEYG 65 (299)
Q Consensus 31 ~I~LrLR~~~-~~~~f~p~~~i~~v~lHELaH~~~~ 65 (299)
.|.+|+..+. +....+.+..| .||.|||-|.+|.
T Consensus 222 ~i~~n~~~~~~~~~~ll~~~~v-~tLfHE~GHa~H~ 256 (458)
T PF01432_consen 222 YIFCNFTGPSAGKPSLLSHDDV-ETLFHEFGHAMHS 256 (458)
T ss_dssp EEEEEE-S-BTTC--B-SHHHH-HHHHHHHHHHHHH
T ss_pred EEEecCCCCCCCCCCccChhhH-HHHHHHHhHHHHH
Confidence 4566666633 22255667777 7999999998764
No 188
>PRK05580 primosome assembly protein PriA; Validated
Probab=20.14 E-value=72 Score=34.01 Aligned_cols=34 Identities=26% Similarity=0.556 Sum_probs=20.2
Q ss_pred cCCcccc----ccccCCccccccCCCCCCCCCCCCCcccCCccc
Q 022290 228 QCNMCTL----LNQPLALTCEACGTQRNKSVGNLKGWSCKFCTL 267 (299)
Q Consensus 228 ~C~~CT~----~N~~~a~~C~aCgt~rp~~~~~~~~W~C~~Ct~ 267 (299)
.|+.|.. .-....+.|.-|+...+. .|.|+.|+-
T Consensus 392 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~------~~~Cp~Cg~ 429 (679)
T PRK05580 392 ECPHCDASLTLHRFQRRLRCHHCGYQEPI------PKACPECGS 429 (679)
T ss_pred CCCCCCCceeEECCCCeEECCCCcCCCCC------CCCCCCCcC
Confidence 4666653 123455678888865432 577888854
No 189
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=20.03 E-value=99 Score=25.47 Aligned_cols=29 Identities=21% Similarity=0.338 Sum_probs=18.6
Q ss_pred CCcccCCcc---cccCCCCccccccCCCCCCC
Q 022290 258 KGWSCKFCT---LDNSSLSERCLACGEWRYSN 286 (299)
Q Consensus 258 ~~W~C~~Ct---~~N~~~~~~C~~Cg~~r~~~ 286 (299)
.++.|+.|+ |--...-.+|.-||+..+..
T Consensus 8 tKR~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 367788887 32222556788888866655
Done!