Query 016954
Match_columns 380
No_of_seqs 336 out of 1688
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 04:19:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016954.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016954hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12315 DUF3633: Protein of u 100.0 1.9E-44 4.1E-49 326.9 8.0 116 265-380 1-116 (212)
2 KOG2272 Focal adhesion protein 99.9 1.5E-29 3.2E-34 233.4 -2.8 167 112-315 72-253 (332)
3 KOG1701 Focal adhesion adaptor 99.9 4E-25 8.6E-30 217.3 -5.1 169 112-311 273-443 (468)
4 KOG1701 Focal adhesion adaptor 99.8 4.7E-21 1E-25 188.6 -0.0 128 106-245 327-462 (468)
5 KOG4577 Transcription factor L 99.8 1.4E-21 3.1E-26 183.5 -4.7 122 112-245 32-153 (383)
6 KOG1703 Adaptor protein Enigma 99.8 2.1E-19 4.5E-24 186.1 7.9 240 111-380 132-372 (479)
7 KOG2272 Focal adhesion protein 99.7 2.7E-18 5.8E-23 159.1 -0.8 124 106-244 188-311 (332)
8 KOG1703 Adaptor protein Enigma 99.7 2.4E-17 5.1E-22 170.8 5.6 173 112-311 302-478 (479)
9 KOG1044 Actin-binding LIM Zn-f 99.6 1.1E-16 2.5E-21 162.6 2.2 118 111-243 131-248 (670)
10 KOG1044 Actin-binding LIM Zn-f 99.6 1E-15 2.2E-20 155.7 5.5 162 112-314 15-190 (670)
11 PF00412 LIM: LIM domain; Int 99.3 9.9E-13 2.2E-17 97.1 3.2 57 116-172 1-58 (58)
12 KOG1700 Regulatory protein MLP 98.8 8.2E-10 1.8E-14 102.2 0.6 122 111-246 5-167 (200)
13 PF00412 LIM: LIM domain; Int 98.6 5E-08 1.1E-12 71.8 3.8 56 176-244 1-56 (58)
14 smart00132 LIM Zinc-binding do 98.4 3.1E-07 6.6E-12 61.6 2.9 37 115-151 1-38 (39)
15 KOG4577 Transcription factor L 97.7 2.2E-06 4.8E-11 81.7 -3.6 69 172-257 32-100 (383)
16 KOG1700 Regulatory protein MLP 97.4 3.2E-05 6.9E-10 71.7 0.2 64 109-172 104-167 (200)
17 KOG1702 Nebulin repeat protein 97.3 2.5E-05 5.4E-10 71.5 -2.0 59 114-172 5-63 (264)
18 smart00132 LIM Zinc-binding do 97.2 0.00027 5.9E-09 47.0 2.5 37 175-222 1-37 (39)
19 KOG0490 Transcription factor, 97.0 0.00012 2.5E-09 68.4 -1.3 114 118-244 1-118 (235)
20 PF14891 Peptidase_M91: Effect 86.5 0.42 9E-06 43.2 1.9 17 358-374 104-120 (174)
21 PF13699 DUF4157: Domain of un 86.4 0.4 8.6E-06 37.9 1.5 19 356-374 60-78 (79)
22 PF13485 Peptidase_MA_2: Pepti 82.7 1.5 3.3E-05 35.8 3.6 24 350-373 18-41 (128)
23 smart00726 UIM Ubiquitin-inter 81.3 1.2 2.6E-05 27.7 1.8 21 43-63 1-21 (26)
24 PF10263 SprT-like: SprT-like 80.8 1.1 2.3E-05 39.3 2.1 22 352-373 55-76 (157)
25 PF06114 DUF955: Domain of unk 79.9 2.1 4.5E-05 34.6 3.4 31 344-374 29-59 (122)
26 PF02809 UIM: Ubiquitin intera 78.6 1 2.2E-05 25.6 0.8 16 43-58 2-17 (18)
27 smart00731 SprT SprT homologue 73.3 2.5 5.4E-05 37.0 2.3 22 353-374 55-76 (146)
28 KOG0320 Predicted E3 ubiquitin 70.1 2.2 4.8E-05 38.8 1.2 50 209-259 128-177 (187)
29 PHA02456 zinc metallopeptidase 68.3 2.8 6.1E-05 35.3 1.4 15 359-373 81-95 (141)
30 PF01447 Peptidase_M4: Thermol 68.2 3 6.4E-05 37.0 1.6 13 358-370 136-148 (150)
31 PF09768 Peptidase_M76: Peptid 67.1 3 6.5E-05 37.9 1.4 19 355-373 69-87 (173)
32 cd04270 ZnMc_TACE_like Zinc-de 67.0 3.4 7.3E-05 39.4 1.8 20 350-369 158-179 (244)
33 KOG1280 Uncharacterized conser 65.8 3.8 8.2E-05 40.9 1.9 73 113-221 8-88 (381)
34 PF04450 BSP: Peptidase of pla 64.9 3.5 7.5E-05 38.5 1.4 15 357-371 96-110 (205)
35 PRK14873 primosome assembly pr 63.9 5.2 0.00011 43.8 2.7 49 113-182 383-431 (665)
36 PF12773 DZR: Double zinc ribb 63.9 6.1 0.00013 27.8 2.3 20 235-254 29-48 (50)
37 PF01421 Reprolysin: Reprolysi 63.0 7.4 0.00016 35.4 3.2 25 344-368 118-142 (199)
38 COG2856 Predicted Zn peptidase 62.7 7.6 0.00016 36.5 3.3 30 344-373 59-88 (213)
39 PF14634 zf-RING_5: zinc-RING 61.8 9.9 0.00021 26.1 3.0 42 215-256 2-43 (44)
40 PF14471 DUF4428: Domain of un 60.9 6.1 0.00013 28.6 1.8 30 214-245 1-30 (51)
41 cd04267 ZnMc_ADAM_like Zinc-de 60.6 5.4 0.00012 36.0 1.9 24 345-369 122-145 (192)
42 TIGR00595 priA primosomal prot 59.2 7.6 0.00017 41.0 2.9 38 142-182 224-262 (505)
43 PF14835 zf-RING_6: zf-RING of 58.7 11 0.00024 28.7 2.9 47 141-187 8-54 (65)
44 PF01435 Peptidase_M48: Peptid 58.5 7.4 0.00016 35.6 2.4 27 345-371 73-103 (226)
45 smart00504 Ubox Modified RING 56.3 9.7 0.00021 27.7 2.3 44 213-259 2-45 (63)
46 PF10367 Vps39_2: Vacuolar sor 56.0 7.4 0.00016 31.4 1.8 13 173-185 78-90 (109)
47 PRK14559 putative protein seri 55.6 11 0.00024 41.1 3.5 9 115-123 3-11 (645)
48 PF10083 DUF2321: Uncharacteri 54.4 6.7 0.00014 35.0 1.3 55 161-228 28-84 (158)
49 PF04228 Zn_peptidase: Putativ 53.6 9.1 0.0002 37.7 2.2 22 354-375 167-188 (292)
50 PF01863 DUF45: Protein of unk 53.4 8.1 0.00018 35.1 1.8 26 344-369 151-176 (205)
51 PF09943 DUF2175: Uncharacteri 52.9 4.5 9.9E-05 33.5 0.0 29 115-143 4-33 (101)
52 smart00235 ZnMc Zinc-dependent 52.8 6.7 0.00015 33.5 1.1 9 360-368 89-97 (140)
53 KOG2199 Signal transducing ada 52.8 9.8 0.00021 38.8 2.3 26 40-65 161-186 (462)
54 PRK04351 hypothetical protein; 52.6 11 0.00023 33.5 2.3 18 357-374 61-78 (149)
55 PF10367 Vps39_2: Vacuolar sor 52.5 13 0.00028 29.9 2.7 30 113-142 78-108 (109)
56 PF12674 Zn_ribbon_2: Putative 51.8 7.8 0.00017 30.8 1.2 31 214-244 2-35 (81)
57 PRK04860 hypothetical protein; 51.2 11 0.00023 33.9 2.1 21 353-373 59-79 (160)
58 PF13688 Reprolysin_5: Metallo 51.0 9.9 0.00022 34.3 1.9 17 353-369 138-154 (196)
59 COG2738 Predicted Zn-dependent 50.6 8.4 0.00018 35.7 1.3 29 350-378 85-113 (226)
60 PF00413 Peptidase_M10: Matrix 50.3 8.9 0.00019 32.9 1.5 16 353-368 101-116 (154)
61 cd00203 ZnMc Zinc-dependent me 50.0 11 0.00024 32.8 2.0 16 354-369 93-108 (167)
62 PRK14890 putative Zn-ribbon RN 49.7 15 0.00032 27.5 2.3 27 113-149 7-34 (59)
63 PF04298 Zn_peptidase_2: Putat 49.6 10 0.00022 35.8 1.8 26 353-378 85-110 (222)
64 cd04268 ZnMc_MMP_like Zinc-dep 49.0 9.2 0.0002 33.3 1.4 13 357-369 94-106 (165)
65 KOG3624 M13 family peptidase [ 48.7 8.4 0.00018 42.1 1.3 15 355-369 516-530 (687)
66 PF11781 RRN7: RNA polymerase 48.6 10 0.00023 25.3 1.2 24 142-169 10-33 (36)
67 PF05572 Peptidase_M43: Pregna 48.6 9.1 0.0002 34.0 1.2 19 353-372 65-83 (154)
68 PF01433 Peptidase_M1: Peptida 48.3 7.6 0.00017 38.7 0.8 14 357-370 295-308 (390)
69 PF13240 zinc_ribbon_2: zinc-r 47.9 11 0.00023 22.7 1.1 8 116-123 2-9 (23)
70 PF08394 Arc_trans_TRASH: Arch 47.2 12 0.00026 25.3 1.4 26 116-141 1-27 (37)
71 KOG0320 Predicted E3 ubiquitin 47.0 7.8 0.00017 35.3 0.6 48 138-185 129-179 (187)
72 PF14247 DUF4344: Domain of un 46.5 14 0.00031 34.8 2.2 21 358-378 93-113 (220)
73 cd06161 S2P-M50_SpoIVFB SpoIVF 45.8 14 0.00029 34.3 2.0 21 355-375 36-57 (208)
74 PF14446 Prok-RING_1: Prokaryo 45.7 12 0.00026 27.5 1.2 29 113-141 5-36 (54)
75 PF06677 Auto_anti-p27: Sjogre 45.6 13 0.00028 25.7 1.4 21 215-241 20-40 (41)
76 PF13574 Reprolysin_2: Metallo 45.5 12 0.00025 33.7 1.5 13 357-369 111-123 (173)
77 PF08219 TOM13: Outer membrane 45.5 15 0.00034 28.8 1.9 16 354-369 49-64 (77)
78 COG1451 Predicted metal-depend 44.9 12 0.00025 35.4 1.4 27 342-368 160-186 (223)
79 cd06159 S2P-M50_PDZ_Arch Uncha 44.7 14 0.00031 35.7 2.0 24 348-372 110-133 (263)
80 KOG0490 Transcription factor, 44.5 12 0.00027 34.4 1.5 52 207-259 18-69 (235)
81 cd06162 S2P-M50_PDZ_SREBP Ster 44.2 15 0.00032 36.0 2.0 17 356-372 134-150 (277)
82 cd04269 ZnMc_adamalysin_II_lik 44.0 22 0.00048 32.1 3.1 16 354-369 128-143 (194)
83 KOG3714 Meprin A metalloprotea 43.8 11 0.00023 38.9 1.0 23 333-369 149-171 (411)
84 PF13920 zf-C3HC4_3: Zinc fing 43.6 15 0.00032 25.8 1.4 42 142-184 4-48 (50)
85 PF13920 zf-C3HC4_3: Zinc fing 43.2 18 0.0004 25.3 1.9 43 214-259 4-47 (50)
86 COG1645 Uncharacterized Zn-fin 43.0 12 0.00027 32.4 1.2 25 214-245 30-54 (131)
87 PF10235 Cript: Microtubule-as 42.8 15 0.00032 29.9 1.5 24 160-185 58-81 (90)
88 PRK14015 pepN aminopeptidase N 42.8 12 0.00026 42.4 1.3 14 357-370 296-309 (875)
89 PRK04897 heat shock protein Ht 42.8 11 0.00024 36.9 1.0 18 351-368 131-148 (298)
90 PRK05580 primosome assembly pr 42.3 20 0.00042 39.4 2.8 38 142-182 392-430 (679)
91 cd06164 S2P-M50_SpoIVFB_CBS Sp 42.2 16 0.00036 34.4 2.0 21 355-375 51-72 (227)
92 COG2191 Formylmethanofuran deh 41.9 12 0.00027 34.7 1.0 15 157-171 189-203 (206)
93 COG4357 Zinc finger domain con 41.9 4.3 9.3E-05 33.3 -1.7 49 116-164 38-86 (105)
94 PRK01345 heat shock protein Ht 41.3 22 0.00048 35.3 2.8 18 352-369 119-136 (317)
95 KOG1702 Nebulin repeat protein 41.0 7.7 0.00017 36.2 -0.4 37 207-245 26-62 (264)
96 cd04279 ZnMc_MMP_like_1 Zinc-d 41.0 14 0.00031 32.2 1.3 14 355-368 102-115 (156)
97 PRK00420 hypothetical protein; 40.9 16 0.00034 30.9 1.4 26 214-245 25-50 (112)
98 PF13639 zf-RING_2: Ring finge 40.3 15 0.00032 25.0 1.0 42 214-255 2-43 (44)
99 COG1645 Uncharacterized Zn-fin 39.6 16 0.00034 31.8 1.2 21 143-168 31-51 (131)
100 KOG3931 Uncharacterized conser 38.6 18 0.00039 36.4 1.6 22 353-374 101-122 (484)
101 TIGR02420 dksA RNA polymerase- 38.6 7.6 0.00017 32.4 -0.8 20 111-131 78-97 (110)
102 PF06037 DUF922: Bacterial pro 38.4 50 0.0011 29.5 4.4 29 345-373 58-102 (161)
103 TIGR02411 leuko_A4_hydro leuko 38.2 15 0.00033 39.7 1.2 12 359-370 281-292 (601)
104 PRK05457 heat shock protein Ht 38.0 16 0.00036 35.6 1.3 19 350-368 127-145 (284)
105 cd04281 ZnMc_BMP1_TLD Zinc-dep 37.7 16 0.00036 33.8 1.2 10 360-369 90-99 (200)
106 COG2888 Predicted Zn-ribbon RN 37.5 11 0.00024 28.2 0.1 10 174-183 10-19 (61)
107 COG4784 Putative Zn-dependent 36.8 19 0.0004 36.4 1.4 46 308-368 85-135 (479)
108 COG1198 PriA Primosomal protei 36.8 30 0.00066 38.3 3.2 39 141-182 445-484 (730)
109 PF00645 zf-PARP: Poly(ADP-rib 36.4 15 0.00033 28.6 0.6 17 111-127 5-21 (82)
110 PRK03001 M48 family peptidase; 36.1 18 0.00038 35.2 1.2 18 352-369 119-136 (283)
111 cd00162 RING RING-finger (Real 36.0 27 0.00058 22.7 1.8 41 215-257 2-43 (45)
112 PRK02870 heat shock protein Ht 35.8 20 0.00043 36.0 1.5 24 345-368 157-184 (336)
113 PRK03982 heat shock protein Ht 35.6 19 0.00041 35.1 1.3 18 352-369 120-137 (288)
114 COG0501 HtpX Zn-dependent prot 35.5 20 0.00044 34.4 1.5 19 351-369 151-169 (302)
115 PRK03072 heat shock protein Ht 35.4 18 0.0004 35.3 1.2 19 350-368 120-138 (288)
116 KOG1813 Predicted E3 ubiquitin 35.0 20 0.00044 35.2 1.4 46 140-186 241-288 (313)
117 COG2191 Formylmethanofuran deh 34.7 15 0.00033 34.1 0.5 30 213-244 173-202 (206)
118 PF13582 Reprolysin_3: Metallo 34.6 21 0.00045 29.5 1.3 11 359-369 109-119 (124)
119 PF10460 Peptidase_M30: Peptid 34.5 21 0.00045 36.3 1.4 13 356-368 138-150 (366)
120 PF09471 Peptidase_M64: IgA Pe 34.5 23 0.00049 34.4 1.6 19 356-374 215-233 (264)
121 TIGR00181 pepF oligoendopeptid 34.2 20 0.00042 38.5 1.3 11 359-369 380-390 (591)
122 PF13583 Reprolysin_4: Metallo 34.1 21 0.00044 33.1 1.2 11 359-369 139-149 (206)
123 PRK02391 heat shock protein Ht 34.0 19 0.0004 35.5 1.0 19 351-369 127-145 (296)
124 PF13923 zf-C3HC4_2: Zinc fing 33.9 39 0.00084 22.3 2.3 37 215-253 1-37 (39)
125 cd04272 ZnMc_salivary_gland_MP 33.6 26 0.00057 32.5 1.9 15 355-369 143-157 (220)
126 cd04282 ZnMc_meprin Zinc-depen 33.6 20 0.00044 34.0 1.1 11 359-369 122-132 (230)
127 TIGR02414 pepN_proteo aminopep 33.2 21 0.00046 40.3 1.4 14 357-370 283-296 (863)
128 cd04278 ZnMc_MMP Zinc-dependen 32.7 19 0.00041 31.5 0.7 15 354-368 104-118 (157)
129 cd04327 ZnMc_MMP_like_3 Zinc-d 32.6 27 0.0006 31.9 1.8 13 357-369 92-104 (198)
130 cd04283 ZnMc_hatching_enzyme Z 32.5 23 0.00049 32.4 1.2 10 359-368 79-88 (182)
131 cd06160 S2P-M50_like_2 Unchara 32.4 37 0.00079 31.0 2.6 22 355-376 39-61 (183)
132 KOG1047 Bifunctional leukotrie 32.1 22 0.00047 38.0 1.1 13 358-370 289-301 (613)
133 PF06689 zf-C4_ClpX: ClpX C4-t 31.9 42 0.00091 23.0 2.2 32 214-245 3-34 (41)
134 COG5549 Predicted Zn-dependent 31.7 23 0.00049 33.3 1.1 37 341-378 171-207 (236)
135 TIGR02412 pepN_strep_liv amino 31.5 25 0.00053 39.6 1.5 13 358-370 288-300 (831)
136 TIGR02289 M3_not_pepF oligoend 31.1 25 0.00054 37.5 1.4 12 359-370 339-350 (549)
137 PF01400 Astacin: Astacin (Pep 30.4 28 0.00061 31.8 1.5 13 357-369 79-91 (191)
138 PRK01265 heat shock protein Ht 30.1 34 0.00073 34.2 2.1 24 345-368 124-151 (324)
139 PF14570 zf-RING_4: RING/Ubox 29.5 39 0.00085 24.2 1.7 32 227-258 14-46 (48)
140 cd02341 ZZ_ZZZ3 Zinc finger, Z 29.1 32 0.00068 24.5 1.2 8 237-244 28-35 (48)
141 PF10026 DUF2268: Predicted Zn 29.1 52 0.0011 30.1 3.0 16 355-370 63-78 (195)
142 PF13834 DUF4193: Domain of un 29.0 17 0.00038 30.0 -0.2 28 213-241 71-98 (99)
143 KOG3314 Ku70-binding protein [ 28.5 32 0.0007 31.1 1.4 15 357-371 91-105 (194)
144 PRK14714 DNA polymerase II lar 28.1 59 0.0013 38.1 3.7 13 361-373 906-918 (1337)
145 PF01258 zf-dskA_traR: Prokary 28.0 6.9 0.00015 25.9 -2.2 9 115-123 5-13 (36)
146 smart00291 ZnF_ZZ Zinc-binding 27.6 49 0.0011 22.8 2.0 8 237-244 29-36 (44)
147 PF15295 CCDC50_N: Coiled-coil 27.5 25 0.00055 30.5 0.6 41 44-86 80-120 (132)
148 cd02249 ZZ Zinc finger, ZZ typ 27.3 48 0.001 23.0 1.9 8 237-244 25-32 (46)
149 PF12725 DUF3810: Protein of u 27.1 32 0.00069 34.2 1.3 19 350-368 189-207 (318)
150 KOG2921 Intramembrane metallop 27.0 39 0.00084 34.7 1.8 24 348-371 119-145 (484)
151 KOG3579 Predicted E3 ubiquitin 26.9 27 0.00059 34.2 0.7 31 114-144 269-299 (352)
152 KOG2661 Peptidase family M48 [ 26.9 39 0.00084 34.0 1.8 16 357-372 275-290 (424)
153 PF13203 DUF2201_N: Putative m 26.8 42 0.00092 32.4 2.1 22 350-371 53-74 (292)
154 COG4740 Predicted metalloprote 26.7 44 0.00096 29.6 1.9 18 347-368 140-157 (176)
155 cd04280 ZnMc_astacin_like Zinc 26.5 31 0.00068 31.1 1.0 10 359-368 76-85 (180)
156 PF12388 Peptidase_M57: Dual-a 26.4 55 0.0012 30.8 2.6 21 349-369 125-145 (211)
157 PF12156 ATPase-cat_bd: Putati 26.2 43 0.00094 26.8 1.7 11 175-185 2-12 (88)
158 PF14569 zf-UDP: Zinc-binding 26.1 49 0.0011 26.2 1.9 14 171-184 7-20 (80)
159 COG3590 PepO Predicted metallo 25.2 19 0.00042 38.5 -0.7 13 357-369 487-499 (654)
160 PHA02768 hypothetical protein; 25.1 23 0.0005 26.1 -0.1 21 211-231 30-50 (55)
161 COG0308 PepN Aminopeptidase N 25.1 49 0.0011 37.4 2.5 13 358-370 308-320 (859)
162 COG5148 RPN10 26S proteasome r 25.0 25 0.00055 32.5 0.1 33 45-77 207-239 (243)
163 PHA00527 hypothetical protein 24.8 1E+02 0.0022 25.8 3.6 13 358-370 74-86 (129)
164 PF10462 Peptidase_M66: Peptid 24.6 35 0.00077 33.8 1.1 14 357-370 193-206 (305)
165 PF03854 zf-P11: P-11 zinc fin 24.5 37 0.0008 24.4 0.9 43 213-259 3-45 (50)
166 PF04502 DUF572: Family of unk 24.2 44 0.00094 33.3 1.7 20 112-131 39-58 (324)
167 cd06459 M3B_Oligoendopeptidase 23.3 42 0.0009 34.0 1.4 13 359-371 224-236 (427)
168 TIGR02290 M3_fam_3 oligoendope 23.2 41 0.0009 36.1 1.4 11 359-369 377-387 (587)
169 PF02031 Peptidase_M7: Strepto 23.2 46 0.00099 28.9 1.3 9 360-368 80-88 (132)
170 cd04273 ZnMc_ADAMTS_like Zinc- 22.8 14 0.0003 34.0 -2.1 14 355-368 138-151 (207)
171 cd02335 ZZ_ADA2 Zinc finger, Z 22.6 70 0.0015 22.6 2.0 8 237-244 26-33 (49)
172 PRK04023 DNA polymerase II lar 22.5 90 0.002 35.8 3.8 38 141-186 639-676 (1121)
173 PRK00420 hypothetical protein; 22.5 53 0.0011 27.8 1.6 10 158-167 37-46 (112)
174 cd02336 ZZ_RSC8 Zinc finger, Z 22.5 78 0.0017 22.2 2.2 30 214-244 2-32 (45)
175 cd04271 ZnMc_ADAM_fungal Zinc- 22.4 32 0.0007 32.4 0.3 11 359-369 147-157 (228)
176 COG0266 Nei Formamidopyrimidin 22.3 1.2E+02 0.0025 29.7 4.1 92 26-140 177-271 (273)
177 PF07191 zinc-ribbons_6: zinc- 22.2 31 0.00067 26.7 0.1 38 142-184 3-41 (70)
178 PF10083 DUF2321: Uncharacteri 22.0 39 0.00084 30.2 0.7 53 112-184 27-79 (158)
179 PF01432 Peptidase_M3: Peptida 21.9 1E+02 0.0022 31.7 4.0 17 358-374 243-259 (458)
180 PF07754 DUF1610: Domain of un 21.9 59 0.0013 19.9 1.3 11 176-186 1-11 (24)
181 COG5152 Uncharacterized conser 21.6 25 0.00054 32.7 -0.6 40 141-181 197-238 (259)
182 KOG2719 Metalloprotease [Gener 21.6 44 0.00096 34.6 1.1 15 355-369 278-292 (428)
183 PF11571 Med27: Mediator compl 21.5 35 0.00076 27.4 0.3 17 167-183 48-64 (90)
184 TIGR02890 spore_yteA sporulati 21.3 32 0.00069 30.8 0.0 32 111-148 84-115 (159)
185 PF04502 DUF572: Family of unk 20.8 67 0.0015 32.0 2.2 13 172-184 76-88 (324)
186 cd04277 ZnMc_serralysin_like Z 20.7 53 0.0011 29.5 1.3 16 354-369 110-125 (186)
187 PF05502 Dynactin_p62: Dynacti 20.4 76 0.0017 33.5 2.6 41 112-153 25-65 (483)
188 KOG2462 C2H2-type Zn-finger pr 20.3 30 0.00064 33.7 -0.4 90 110-222 158-253 (279)
189 TIGR00570 cdk7 CDK-activating 20.2 83 0.0018 31.3 2.7 28 232-259 25-53 (309)
190 PLN02195 cellulose synthase A 20.0 80 0.0017 36.1 2.8 53 111-184 4-59 (977)
No 1
>PF12315 DUF3633: Protein of unknown function (DUF3633); InterPro: IPR022087 This domain family is found in bacteria and eukaryotes, and is approximately 210 amino acids in length. The family is found in association with PF00412 from PFAM.
Probab=100.00 E-value=1.9e-44 Score=326.95 Aligned_cols=116 Identities=72% Similarity=1.148 Sum_probs=114.3
Q ss_pred HhcccccCcccchhhhHHHHHHHhcCCCCCCCCCcccCCcccccccccceeeccccCCCCCccccccccccccccceeEE
Q 016954 265 SIHMKLEQQIPLLLVERQALNEARDGEKNGYYHMPETRGLCLSEEQTVTTVLWRPRFGPGNQARNIITEPYKLTRRCDVT 344 (380)
Q Consensus 265 ~~~~~i~~~~p~~lv~~~aLn~~~~~e~~g~~~~~e~rGl~~~E~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~ 344 (380)
+|||||++++||+||+++|||+|.++|++|++|.++|||||+||+++|++|+|+|++|+|+++++|.|+|++++++|+||
T Consensus 1 ~lnmki~q~~PllLVe~~aLN~a~~~Ek~~~~~~~~tRGLclseeq~v~sv~~~p~~~~~~~~~~~~~e~~~~~~~~eV~ 80 (212)
T PF12315_consen 1 GLNMKIEQEIPLLLVERQALNEAEEGEKIGHHHMPETRGLCLSEEQTVTSVLRRPRMGPGNQLIDMSTEPQRLTRGCEVT 80 (212)
T ss_pred CCCCcccCCCCeEEecHHHHHHHHhhccCCCCCCeeeeeeeeeeeEEEEEEEecCCcCCCCccceeeecceeeccceeEE
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEecCCChhhhhhHHHHHhHHHHhhhcCCCCCCC
Q 016954 345 AILILYGLPRLLTGTILAHEMMHGWMRLQGAFCLFP 380 (380)
Q Consensus 345 ~il~l~glp~~~~g~ilahe~~ha~l~l~g~~~l~~ 380 (380)
+|||||||||++||||||||||||||||+||++|+|
T Consensus 81 ~Ilvl~GLPrll~gsiLAHE~mHa~Lrl~g~~~L~~ 116 (212)
T PF12315_consen 81 AILVLYGLPRLLTGSILAHELMHAWLRLNGFPNLSP 116 (212)
T ss_pred EEEEECCCCHHHHhhHHHHHHHHHHhcccCCCCCCh
Confidence 999999999999999999999999999999999986
No 2
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.94 E-value=1.5e-29 Score=233.41 Aligned_cols=167 Identities=25% Similarity=0.538 Sum_probs=148.6
Q ss_pred CCCccccCCcccccCceEeeCCceecCCCcccCCCCCCCCCceeeccCCccccccccccc-----ccccccccCCcccCC
Q 016954 112 GYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREH-----YHPKCDVCKHFIPSN 186 (380)
Q Consensus 112 ~~~~C~~C~~~I~~g~~v~alg~~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~cy~~~-----f~pkC~~C~~~I~~~ 186 (380)
.+|.|++|++.| .|++|.+|+.+|||.||+|..|++.|.+..|+...|+.+|..|..+. -...|..|+..|..+
T Consensus 72 faPcC~kC~EFi-iGrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~ 150 (332)
T KOG2272|consen 72 FAPCCGKCGEFI-IGRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQ 150 (332)
T ss_pred hchhhcccccch-hhHHHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccc
Confidence 568999999999 79999999999999999999999999999999999999999998763 234799999999864
Q ss_pred CCcceEEecccccccccCCCCccCCCCcccccCCcCCCCCceEEccCCcccChhhhhhhccCCCCCCcchHHHHHHHHHh
Q 016954 187 HGGLIEYRAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAYVALDDGRKLCLECLDSAIMDTNECQPLYLDIQEFYESI 266 (380)
Q Consensus 187 ~~~~i~~~~~~fw~qkycp~h~H~~CF~C~~C~r~l~~g~~f~~l~dg~~~C~~C~~~~v~~~~~C~~c~~~I~~f~e~~ 266 (380)
.+.+++.|| |+.+|+|..|++.|.++.+-+ .|.+||+.|+++ |..++|.+|+++|.
T Consensus 151 ---~l~fr~d~y----------H~yHFkCt~C~keL~sdaRev---k~eLyClrChD~--mgipiCgaC~rpIe------ 206 (332)
T KOG2272|consen 151 ---PLTFRGDPY----------HPYHFKCTTCGKELTSDAREV---KGELYCLRCHDK--MGIPICGACRRPIE------ 206 (332)
T ss_pred ---cccccCCCC----------Cccceecccccccccchhhhh---ccceeccccccc--cCCcccccccCchH------
Confidence 589999875 888899999999998887755 789999999999 99999999996664
Q ss_pred cccccCcccchhhhHHHHHHHh----------cCCCCCCCCCcccCCccccccccccee
Q 016954 267 HMKLEQQIPLLLVERQALNEAR----------DGEKNGYYHMPETRGLCLSEEQTVTTV 315 (380)
Q Consensus 267 ~~~i~~~~p~~lv~~~aLn~~~----------~~e~~g~~~~~e~rGl~~~E~~~~~~~ 315 (380)
.++ +.|||++| +++|.||+|| |++||+|||+||+..+
T Consensus 207 -----erv------i~amgKhWHveHFvCa~CekPFlGHrHY-EkkGlaYCe~h~~qLf 253 (332)
T KOG2272|consen 207 -----ERV------IFAMGKHWHVEHFVCAKCEKPFLGHRHY-EKKGLAYCETHYHQLF 253 (332)
T ss_pred -----HHH------HHHhccccchhheeehhcCCcccchhhh-hhcCchhHHHHHHHHh
Confidence 444 78999999 4578999998 9999999999998775
No 3
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.88 E-value=4e-25 Score=217.25 Aligned_cols=169 Identities=22% Similarity=0.459 Sum_probs=141.1
Q ss_pred CCCccccCCccccc-CceEeeCCceecCCCcccCCCCCCCCCceeeccCCcccccccccccccccccccCCcccCCCCcc
Q 016954 112 GYRICAGCNNEIGH-GRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREHYHPKCDVCKHFIPSNHGGL 190 (380)
Q Consensus 112 ~~~~C~~C~~~I~~-g~~v~alg~~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~cy~~~f~pkC~~C~~~I~~~~~~~ 190 (380)
.+.+|++|++.|.. +..+.||++.||..||+|..|++.|.++.||..|+++||+.||... ..||.+|++.|.+. +
T Consensus 273 ~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~t-lekC~~Cg~~I~d~---i 348 (468)
T KOG1701|consen 273 YFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDT-LEKCNKCGEPIMDR---I 348 (468)
T ss_pred hhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHH-HHHHhhhhhHHHHH---H
Confidence 45699999999953 4568999999999999999999999999999999999999999876 78999999999964 6
Q ss_pred eEEecccccccccCCCCccCCCCcccccCCcCCCCCceEEccCCcccChhhhhhhccCCCCCCcchHHHHHHHHHhcccc
Q 016954 191 IEYRAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAYVALDDGRKLCLECLDSAIMDTNECQPLYLDIQEFYESIHMKL 270 (380)
Q Consensus 191 i~~~~~~fw~qkycp~h~H~~CF~C~~C~r~l~~g~~f~~l~dg~~~C~~C~~~~v~~~~~C~~c~~~I~~f~e~~~~~i 270 (380)
+.+.++. ||++||+|.+|.|.| .|..|+...++++||..||++ .++++|+.|.++| ||-
T Consensus 349 LrA~Gka----------yHp~CF~Cv~C~r~l-dgipFtvd~~n~v~Cv~dfh~--kfAPrCs~C~~PI--------~P~ 407 (468)
T KOG1701|consen 349 LRALGKA----------YHPGCFTCVVCARCL-DGIPFTVDSQNNVYCVPDFHK--KFAPRCSVCGNPI--------LPR 407 (468)
T ss_pred HHhcccc----------cCCCceEEEEecccc-CCccccccCCCceeeehhhhh--hcCcchhhccCCc--------cCC
Confidence 7777754 599999999999998 799999999999999999999 7899999999999 455
Q ss_pred cCcccchhhhHHHHHHHhcCCCCCCCCCcccCCcccc-cccc
Q 016954 271 EQQIPLLLVERQALNEARDGEKNGYYHMPETRGLCLS-EEQT 311 (380)
Q Consensus 271 ~~~~p~~lv~~~aLn~~~~~e~~g~~~~~e~rGl~~~-E~~~ 311 (380)
+++-. .|.+.||++-+|.+.. +. |.-|+-|| |+.-
T Consensus 408 ~G~~e--tvRvvamdr~fHv~CY---~C-EDCg~~LS~e~e~ 443 (468)
T KOG1701|consen 408 DGKDE--TVRVVAMDRDFHVNCY---KC-EDCGLLLSSEEEG 443 (468)
T ss_pred CCCcc--eEEEEEccccccccce---eh-hhcCccccccCCC
Confidence 43321 2455678888877653 32 66677777 4443
No 4
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.80 E-value=4.7e-21 Score=188.64 Aligned_cols=128 Identities=26% Similarity=0.567 Sum_probs=112.4
Q ss_pred ccCCCCCCCccccCCcccccCceEeeCCceecCCCcccCCCCCCCCCceeec-cCCcccccccccccccccccccCCccc
Q 016954 106 VIQFPEGYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFST-SENRPYHKSCYREHYHPKCDVCKHFIP 184 (380)
Q Consensus 106 ~~~~~~~~~~C~~C~~~I~~g~~v~alg~~wH~~CF~C~~C~~~L~~~~f~~-~dg~~YC~~cy~~~f~pkC~~C~~~I~ 184 (380)
+..+..+..+|..|++.| .++++.|+|+.||+.||+|..|.+.|.+..|.+ .++++||-.||+++|+|+|.+|+++|.
T Consensus 327 E~cyq~tlekC~~Cg~~I-~d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~ 405 (468)
T KOG1701|consen 327 EGCYQDTLEKCNKCGEPI-MDRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPIL 405 (468)
T ss_pred hHHHHHHHHHHhhhhhHH-HHHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCcc
Confidence 445666788999999999 689999999999999999999999999999987 588999999999999999999999999
Q ss_pred CCCCc----ceEEecccccccccCCCCccCCCCcccccCCcCC---CCCceEEccCCcccChhhhhhh
Q 016954 185 SNHGG----LIEYRAHPFWVQKYCPSHEHDGTPRCCSCERMEP---QDTAYVALDDGRKLCLECLDSA 245 (380)
Q Consensus 185 ~~~~~----~i~~~~~~fw~qkycp~h~H~~CF~C~~C~r~l~---~g~~f~~l~dg~~~C~~C~~~~ 245 (380)
+.++. .|+.+++.| |.+|++|..|+.+|. .+..+|.| ||+++|+.|+.+.
T Consensus 406 P~~G~~etvRvvamdr~f----------Hv~CY~CEDCg~~LS~e~e~qgCyPl-d~HllCk~Ch~~R 462 (468)
T KOG1701|consen 406 PRDGKDETVRVVAMDRDF----------HVNCYKCEDCGLLLSSEEEGQGCYPL-DGHLLCKTCHLKR 462 (468)
T ss_pred CCCCCcceEEEEEccccc----------cccceehhhcCccccccCCCCcceec-cCceeechhhhhh
Confidence 87532 567777664 999999999999886 46778887 9999999998764
No 5
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.79 E-value=1.4e-21 Score=183.49 Aligned_cols=122 Identities=30% Similarity=0.629 Sum_probs=110.0
Q ss_pred CCCccccCCcccccCceEeeCCceecCCCcccCCCCCCCCCceeeccCCcccccccccccccccccccCCcccCCCCcce
Q 016954 112 GYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREHYHPKCDVCKHFIPSNHGGLI 191 (380)
Q Consensus 112 ~~~~C~~C~~~I~~g~~v~alg~~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~cy~~~f~pkC~~C~~~I~~~~~~~i 191 (380)
..++|++|.+-|.+..++.++++.||..|++|+.|..+|.+..|. ++|.+||+.+|.++|+.||..|+..|++.. |
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~drCFs-R~~s~yCkedFfKrfGTKCsaC~~GIpPtq---V 107 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADRCFS-REGSVYCKEDFFKRFGTKCSACQEGIPPTQ---V 107 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHHHhh-cCCceeehHHHHHHhCCcchhhcCCCChHH---H
Confidence 678999999999655667999999999999999999999998776 688999999999999999999999999864 5
Q ss_pred EEecccccccccCCCCccCCCCcccccCCcCCCCCceEEccCCcccChhhhhhh
Q 016954 192 EYRAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAYVALDDGRKLCLECLDSA 245 (380)
Q Consensus 192 ~~~~~~fw~qkycp~h~H~~CF~C~~C~r~l~~g~~f~~l~dg~~~C~~C~~~~ 245 (380)
+.+++.| .||..||.|..|.|.|..|+.||.+.|++++|+..|+++
T Consensus 108 VRkAqd~--------VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~A 153 (383)
T KOG4577|consen 108 VRKAQDF--------VYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETA 153 (383)
T ss_pred HHHhhcc--------eeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHH
Confidence 5555554 579999999999999999999999999999999999985
No 6
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.78 E-value=2.1e-19 Score=186.09 Aligned_cols=240 Identities=49% Similarity=0.856 Sum_probs=209.0
Q ss_pred CCCCccccCCcccccCceEeeCCceecCCCcccCCCCCCCCCceeeccCCcccccccccc-cccccccccCCcccCCCCc
Q 016954 111 EGYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYRE-HYHPKCDVCKHFIPSNHGG 189 (380)
Q Consensus 111 ~~~~~C~~C~~~I~~g~~v~alg~~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~cy~~-~f~pkC~~C~~~I~~~~~~ 189 (380)
....+|.+|...|..+..+ ||.|..|..++.+ +-..+|.. ...+.+.++...|..+..+
T Consensus 132 ~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~p~~~----------~~~~~~~~~~~~~~~~v~~~~~~~~~~~ 191 (479)
T KOG1703|consen 132 PLDSICGGCNSAIEHGRSV----------CFQCKRCSEPLSG----------FPKPSYHESGRSKNEDVEEASSPSSRAG 191 (479)
T ss_pred cccccccCCCcccccccch----------hhhhcccccccCC----------cccccccccccccccccccccccccccc
Confidence 3557799999998766555 8888888888722 22334444 3567899999999988778
Q ss_pred ceEEecccccccccCCCCccCCCCcccccCCcCCCCCceEEccCCcccChhhhhhhccCCCCCCcchHHHHHHHHHhccc
Q 016954 190 LIEYRAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAYVALDDGRKLCLECLDSAIMDTNECQPLYLDIQEFYESIHMK 269 (380)
Q Consensus 190 ~i~~~~~~fw~qkycp~h~H~~CF~C~~C~r~l~~g~~f~~l~dg~~~C~~C~~~~v~~~~~C~~c~~~I~~f~e~~~~~ 269 (380)
.+.++.++||.++||+.|.++.+..|+.|.+.++.+..++.+.+++.+|.+|....+|+.++|++....+..+++...++
T Consensus 192 ~~~~~~~~~~~~~~~~~~e~~~tp~~~~~~r~e~~~~~~~~l~~~~~~~~~~~~~~~~~~p~~~p~~~~~~~~~~~~~~~ 271 (479)
T KOG1703|consen 192 LILSRSHPFWKQKYCPSHENDGTPKCCSCERLEPLDTRYVELADGRALCLECMGSASMDSPECQPLVSAPRPASEGLHMK 271 (479)
T ss_pred ccccccchhhhhcccccccCCCCCCcccccccccccccceecccchhhhhhccCCcccCCCccCcceecccccccccccc
Confidence 88999999999999999999999999999998867888999999999999999888899999999999999999999999
Q ss_pred ccCcccchhhhHHHHHHHhcCCCCCCCCCcccCCcccccccccceeeccccCCCCCccccccccccccccceeEEEEEEe
Q 016954 270 LEQQIPLLLVERQALNEARDGEKNGYYHMPETRGLCLSEEQTVTTVLWRPRFGPGNQARNIITEPYKLTRRCDVTAILIL 349 (380)
Q Consensus 270 i~~~~p~~lv~~~aLn~~~~~e~~g~~~~~e~rGl~~~E~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~il~l 349 (380)
+++..+++++++.+++++-........|. .++++|.++.++++++ ..++++.++..+....|+|++|+++
T Consensus 272 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~p~c~~c~~~i~~~---------~~i~~~~~~~h~~~~~c~~~~~~~~ 341 (479)
T KOG1703|consen 272 VEKELPLLLVESEALKKLREEEKPAEYHN-VTRPLCLSCNQKIRSV---------KVIVALGKEWHPEHFSCEVCAIVIL 341 (479)
T ss_pred cccccchhhcccccccccccccccccccc-cccccccccccCcccc---------eeEeeccccccccceeecccccccc
Confidence 99999999999999999998877666554 8899999999998664 3466888888888999999999999
Q ss_pred cCCChhhhhhHHHHHhHHHHhhhcCCCCCCC
Q 016954 350 YGLPRLLTGTILAHEMMHGWMRLQGAFCLFP 380 (380)
Q Consensus 350 ~glp~~~~g~ilahe~~ha~l~l~g~~~l~~ 380 (380)
+|+|++.+|.|++||+||+|++.++++.+.|
T Consensus 342 ~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~ 372 (479)
T KOG1703|consen 342 DGGPRELDGKILCHECFHAPFRPNCKRCLLP 372 (479)
T ss_pred CCCccccCCCccHHHHHHHhhCccccccCCc
Confidence 9999999999999999999999999887764
No 7
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.68 E-value=2.7e-18 Score=159.07 Aligned_cols=124 Identities=20% Similarity=0.506 Sum_probs=111.1
Q ss_pred ccCCCCCCCccccCCcccccCceEeeCCceecCCCcccCCCCCCCCCceeeccCCcccccccccccccccccccCCcccC
Q 016954 106 VIQFPEGYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREHYHPKCDVCKHFIPS 185 (380)
Q Consensus 106 ~~~~~~~~~~C~~C~~~I~~g~~v~alg~~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~cy~~~f~pkC~~C~~~I~~ 185 (380)
..+...+.++|+.|.++| .+++|.+||+.||.+.|+|+.|.+|+-+...|+..|.+||+.+|.++|+..|..|+..|.+
T Consensus 188 rChD~mgipiCgaC~rpI-eervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G 266 (332)
T KOG2272|consen 188 RCHDKMGIPICGACRRPI-EERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGG 266 (332)
T ss_pred ccccccCCcccccccCch-HHHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhheecCCccCc
Confidence 344557899999999999 7999999999999999999999999999999999999999999999999999999999997
Q ss_pred CCCcceEEecccccccccCCCCccCCCCcccccCCcCCCCCceEEccCCcccChhhhhh
Q 016954 186 NHGGLIEYRAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAYVALDDGRKLCLECLDS 244 (380)
Q Consensus 186 ~~~~~i~~~~~~fw~qkycp~h~H~~CF~C~~C~r~l~~g~~f~~l~dg~~~C~~C~~~ 244 (380)
. ++.+.++. |=+.||.|+.|.+.+..-++|+.+ |-.++|+.||++
T Consensus 267 ~---vv~al~Ka----------wCv~cf~Cs~Cdkkl~~K~Kf~E~-DmkP~CKkCy~r 311 (332)
T KOG2272|consen 267 D---VVSALNKA----------WCVECFSCSTCDKKLTQKNKFYEF-DMKPVCKKCYDR 311 (332)
T ss_pred c---HHHHhhhh----------hccccccccccccccccccceeee-ccchHHHHHHhh
Confidence 6 36666543 356789999999999888899976 889999999996
No 8
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.68 E-value=2.4e-17 Score=170.79 Aligned_cols=173 Identities=18% Similarity=0.326 Sum_probs=138.7
Q ss_pred CCCccccCCcccccC-ceEeeCCceecCCCcccCCCCCCCCCceeeccCCcccccccccccccccccccCCcccCCCCcc
Q 016954 112 GYRICAGCNNEIGHG-RFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREHYHPKCDVCKHFIPSNHGGL 190 (380)
Q Consensus 112 ~~~~C~~C~~~I~~g-~~v~alg~~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~cy~~~f~pkC~~C~~~I~~~~~~~ 190 (380)
..+.|..|++.| .+ +++.++++.||+.+|.|..|...|....|...+|++||..||.+.+.|+|..|+.+|.++.
T Consensus 302 ~~p~c~~c~~~i-~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~--- 377 (479)
T KOG1703|consen 302 TRPLCLSCNQKI-RSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEG--- 377 (479)
T ss_pred ccccccccccCc-ccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHhH---
Confidence 458999999999 56 9999999999999999999999999989999999999999999999999999999999864
Q ss_pred eEEecccccccccCCCCccCCCCcccccCCcCCCCCceEEccCCcccChhhhhhhccCCCCCCcchHHHH---HHHHHhc
Q 016954 191 IEYRAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAYVALDDGRKLCLECLDSAIMDTNECQPLYLDIQ---EFYESIH 267 (380)
Q Consensus 191 i~~~~~~fw~qkycp~h~H~~CF~C~~C~r~l~~g~~f~~l~dg~~~C~~C~~~~v~~~~~C~~c~~~I~---~f~e~~~ 267 (380)
|.+.+ .+||++||.|..|++.+ .+..|+ +.+|.+||..||.. .++..|..|..+|. .+.++++
T Consensus 378 v~a~~----------~~wH~~cf~C~~C~~~~-~~~~~~-~~~~~pyce~~~~~--~~~~~~~~~~~p~~~~~~~ie~~~ 443 (479)
T KOG1703|consen 378 VCALG----------RLWHPECFVCADCGKPL-KNSSFF-ESDGEPYCEDHYKK--LFTTKCDYCKKPVEFGSRQIEADG 443 (479)
T ss_pred hhhcc----------CeechhceeeecccCCC-CCCccc-ccCCccchhhhHhh--hccccchhccchhHhhhhHhhccC
Confidence 55554 46899999999998888 455566 57999999999999 45679999988775 4445566
Q ss_pred ccccCcccchhhhHHHHHHHhcCCCCCCCCCcccCCcccccccc
Q 016954 268 MKLEQQIPLLLVERQALNEARDGEKNGYYHMPETRGLCLSEEQT 311 (380)
Q Consensus 268 ~~i~~~~p~~lv~~~aLn~~~~~e~~g~~~~~e~rGl~~~E~~~ 311 (380)
-++...... ....+++.++. .++++.+.+||..+.
T Consensus 444 ~~~h~~~F~----c~~c~~~l~~~-----~~~~~~~~p~c~~~~ 478 (479)
T KOG1703|consen 444 SPFHGDCFR----CANCMKKLTKK-----TFFETLDKPLCQKHF 478 (479)
T ss_pred cccccccee----hhhhhccccCC-----ceeecCCccccccCC
Confidence 666544321 23333333332 346888889987664
No 9
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.62 E-value=1.1e-16 Score=162.57 Aligned_cols=118 Identities=28% Similarity=0.656 Sum_probs=106.0
Q ss_pred CCCCccccCCcccccCceEeeCCceecCCCcccCCCCCCCCCceeeccCCcccccccccccccccccccCCcccCCCCcc
Q 016954 111 EGYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREHYHPKCDVCKHFIPSNHGGL 190 (380)
Q Consensus 111 ~~~~~C~~C~~~I~~g~~v~alg~~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~cy~~~f~pkC~~C~~~I~~~~~~~ 190 (380)
.+...|++|++.|-.|..+.|+++.||..||+|..|+..|.+ +|..+||.|||+.||.+.|+-+|..|.++|.+..
T Consensus 131 ~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~g-ey~skdg~pyce~dy~~~fgvkc~~c~~fisgkv--- 206 (670)
T KOG1044|consen 131 YGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNG-EYMSKDGVPYCEKDYQAKFGVKCEECEKFISGKV--- 206 (670)
T ss_pred cCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccc-eeeccCCCcchhhhhhhhcCeehHHhhhhhhhhh---
Confidence 366789999999988999999999999999999999999976 7889999999999999999999999999999853
Q ss_pred eEEecccccccccCCCCccCCCCcccccCCcCCCCCceEEccCCcccChhhhh
Q 016954 191 IEYRAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAYVALDDGRKLCLECLD 243 (380)
Q Consensus 191 i~~~~~~fw~qkycp~h~H~~CF~C~~C~r~l~~g~~f~~l~dg~~~C~~C~~ 243 (380)
+.+-+ .|||+.|-+|..|+.+|..|+.-| |....++-..|-.
T Consensus 207 Lqag~----------kh~HPtCARCsRCgqmF~eGEEMY-lQGs~iWHP~C~q 248 (670)
T KOG1044|consen 207 LQAGD----------KHFHPTCARCSRCGQMFGEGEEMY-LQGSEIWHPDCKQ 248 (670)
T ss_pred hhccC----------cccCcchhhhhhhccccccchhee-eccccccCCcccc
Confidence 66655 478999999999999999999887 6677888888865
No 10
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.58 E-value=1e-15 Score=155.74 Aligned_cols=162 Identities=17% Similarity=0.312 Sum_probs=129.7
Q ss_pred CCCccccCCcccccCceEeeCCceecCCCcccCCCCCCCCCceeeccCCcccccccccccccccccccCCcccCCCCcce
Q 016954 112 GYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREHYHPKCDVCKHFIPSNHGGLI 191 (380)
Q Consensus 112 ~~~~C~~C~~~I~~g~~v~alg~~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~cy~~~f~pkC~~C~~~I~~~~~~~i 191 (380)
....|.+|.+.. .|+++.+.++.||..||+|..|+..|...+|+..++. .++++ ..|.++|.++. |
T Consensus 15 ~~i~c~~c~~kc-~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~--------~~ygt--~~c~~~~~gev---v 80 (670)
T KOG1044|consen 15 QGIKCDKCRKKC-SGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPEN--------RLYGT--DDCRAFVEGEV---V 80 (670)
T ss_pred cceehhhhCCcc-ccceeEeeccccceeeeeccccCCCcccccceecccc--------eeecc--cchhhhcccee---E
Confidence 346799999999 7999999999999999999999999999999887765 44555 77999999864 7
Q ss_pred EEecccccccccCCCCccCCCCcccccCCcCCCCCceEEccCCcccChhhhhhhcc------CCCCCCcchHHHHHHHHH
Q 016954 192 EYRAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAYVALDDGRKLCLECLDSAIM------DTNECQPLYLDIQEFYES 265 (380)
Q Consensus 192 ~~~~~~fw~qkycp~h~H~~CF~C~~C~r~l~~g~~f~~l~dg~~~C~~C~~~~v~------~~~~C~~c~~~I~~f~e~ 265 (380)
.+.++. ||++||.|+.|..+++.|++.. +.....+|..|-...-. +...|++|..+|..
T Consensus 81 sa~gkt----------yh~~cf~cs~ck~pf~~g~~vt-~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~---- 145 (670)
T KOG1044|consen 81 STLGKT----------YHPKCFSCSTCKSPFKSGDKVT-FSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKN---- 145 (670)
T ss_pred ecccce----------eccccceecccCCCCCCCCeee-ecchhhhhhhhcCcccCCcccccCCccccchhhhhhc----
Confidence 888754 5999999999999999998854 66777899999764321 45789999988862
Q ss_pred hcccccCcccchhhhHHHHHHHhcCC--------CCCCCCCcccCCcccccccccce
Q 016954 266 IHMKLEQQIPLLLVERQALNEARDGE--------KNGYYHMPETRGLCLSEEQTVTT 314 (380)
Q Consensus 266 ~~~~i~~~~p~~lv~~~aLn~~~~~e--------~~g~~~~~e~rGl~~~E~~~~~~ 314 (380)
+|. .-||.++|+.- ...++.|+.++|++|||++|+.-
T Consensus 146 ------gq~------llald~qwhv~cfkc~~c~~vL~gey~skdg~pyce~dy~~~ 190 (670)
T KOG1044|consen 146 ------GQA------LLALDKQWHVSCFKCKSCSAVLNGEYMSKDGVPYCEKDYQAK 190 (670)
T ss_pred ------cce------eeeeccceeeeeeehhhhcccccceeeccCCCcchhhhhhhh
Confidence 333 24777777653 23455678999999999999754
No 11
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.31 E-value=9.9e-13 Score=97.11 Aligned_cols=57 Identities=37% Similarity=1.023 Sum_probs=52.1
Q ss_pred cccCCcccccCceE-eeCCceecCCCcccCCCCCCCCCceeeccCCcccccccccccc
Q 016954 116 CAGCNNEIGHGRFL-NCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREHY 172 (380)
Q Consensus 116 C~~C~~~I~~g~~v-~alg~~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~cy~~~f 172 (380)
|.+|+++|..+..+ .++|+.||++||+|..|+++|.+..|+..+|++||+.||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 88999999766655 7999999999999999999999988999999999999998765
No 12
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=98.82 E-value=8.2e-10 Score=102.20 Aligned_cols=122 Identities=22% Similarity=0.447 Sum_probs=91.8
Q ss_pred CCCCccccCCcccccCceEeeCCceecCCCcccCCCCCCCCCceeeccCCccccccccccccccc---------------
Q 016954 111 EGYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREHYHPK--------------- 175 (380)
Q Consensus 111 ~~~~~C~~C~~~I~~g~~v~alg~~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~cy~~~f~pk--------------- 175 (380)
.....|..|++.++..+.+...|..||+.||+|..|...|....+..+++.+||+.||-.+++|+
T Consensus 5 ~~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~ 84 (200)
T KOG1700|consen 5 GTTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLG 84 (200)
T ss_pred cccchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCC
Confidence 45568999999998888888999999999999999999999999999999999999765544443
Q ss_pred --------------------------ccccCCcccCCCCcceEEecccccccccCCCCccCCCCcccccCCcCCCCCceE
Q 016954 176 --------------------------CDVCKHFIPSNHGGLIEYRAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAYV 229 (380)
Q Consensus 176 --------------------------C~~C~~~I~~~~~~~i~~~~~~fw~qkycp~h~H~~CF~C~~C~r~l~~g~~f~ 229 (380)
|..|++++-+.. -+...+ .-||..||+|+.|+..+. ...|.
T Consensus 85 ~~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~E--k~~~~~----------~~~hk~cfrc~~~~~~ls-~~~~~ 151 (200)
T KOG1700|consen 85 KDGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLE--KVTGNG----------LEFHKSCFRCTHCGKKLS-PKNYA 151 (200)
T ss_pred cccccccccccccchhHHhhhccccccccccceeeehH--HHhhhh----------hhhhhhheeecccccccC-Ccchh
Confidence 555555444321 122222 246999999999999885 44555
Q ss_pred EccCCcccChhhhhhhc
Q 016954 230 ALDDGRKLCLECLDSAI 246 (380)
Q Consensus 230 ~l~dg~~~C~~C~~~~v 246 (380)
..+|.++|...+-.+.
T Consensus 152 -~~~g~l~~~~~~~~~~ 167 (200)
T KOG1700|consen 152 -ALEGVLYCKHHFAQLF 167 (200)
T ss_pred -hcCCccccchhhheee
Confidence 4578888877666543
No 13
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=98.58 E-value=5e-08 Score=71.79 Aligned_cols=56 Identities=20% Similarity=0.456 Sum_probs=44.0
Q ss_pred ccccCCcccCCCCcceEEecccccccccCCCCccCCCCcccccCCcCCCCCceEEccCCcccChhhhhh
Q 016954 176 CDVCKHFIPSNHGGLIEYRAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAYVALDDGRKLCLECLDS 244 (380)
Q Consensus 176 C~~C~~~I~~~~~~~i~~~~~~fw~qkycp~h~H~~CF~C~~C~r~l~~g~~f~~l~dg~~~C~~C~~~ 244 (380)
|..|+++|.+.. ..+.+.++ .||+.||+|..|+++|..+. |+ ..+|++||..||.+
T Consensus 1 C~~C~~~I~~~~-~~~~~~~~----------~~H~~Cf~C~~C~~~l~~~~-~~-~~~~~~~C~~c~~~ 56 (58)
T PF00412_consen 1 CARCGKPIYGTE-IVIKAMGK----------FWHPECFKCSKCGKPLNDGD-FY-EKDGKPYCKDCYQK 56 (58)
T ss_dssp BTTTSSBESSSS-EEEEETTE----------EEETTTSBETTTTCBTTTSS-EE-EETTEEEEHHHHHH
T ss_pred CCCCCCCccCcE-EEEEeCCc----------EEEccccccCCCCCccCCCe-eE-eECCEEECHHHHhh
Confidence 789999999764 22245553 46999999999999996554 66 46899999999986
No 14
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=98.36 E-value=3.1e-07 Score=61.63 Aligned_cols=37 Identities=46% Similarity=1.106 Sum_probs=33.3
Q ss_pred ccccCCcccccC-ceEeeCCceecCCCcccCCCCCCCC
Q 016954 115 ICAGCNNEIGHG-RFLNCLDVFWHPECFCCHACHQPIT 151 (380)
Q Consensus 115 ~C~~C~~~I~~g-~~v~alg~~wH~~CF~C~~C~~~L~ 151 (380)
+|.+|+++|..+ ..+.++++.||+.||+|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 589999999655 7788999999999999999999985
No 15
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=97.71 E-value=2.2e-06 Score=81.73 Aligned_cols=69 Identities=17% Similarity=0.325 Sum_probs=55.4
Q ss_pred ccccccccCCcccCCCCcceEEecccccccccCCCCccCCCCcccccCCcCCCCCceEEccCCcccChhhhhhhccCCCC
Q 016954 172 YHPKCDVCKHFIPSNHGGLIEYRAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAYVALDDGRKLCLECLDSAIMDTNE 251 (380)
Q Consensus 172 f~pkC~~C~~~I~~~~~~~i~~~~~~fw~qkycp~h~H~~CF~C~~C~r~l~~g~~f~~l~dg~~~C~~C~~~~v~~~~~ 251 (380)
--|+|..|++.|.+.- ++...+ +|||..|.+|+.|..+| +++++ ..+|.+||+++|.+ .+..+
T Consensus 32 eip~CagC~q~IlDrF--ilKvl~----------R~wHs~CLkCs~C~~qL--~drCF-sR~~s~yCkedFfK--rfGTK 94 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRF--ILKVLD----------RHWHSSCLKCSDCHDQL--ADRCF-SREGSVYCKEDFFK--RFGTK 94 (383)
T ss_pred ccccccchHHHHHHHH--HHHHHh----------hhhhhhhcchhhhhhHH--HHHHh-hcCCceeehHHHHH--HhCCc
Confidence 4689999999998642 223333 68999999999999877 56666 46999999999998 57889
Q ss_pred CCcchH
Q 016954 252 CQPLYL 257 (380)
Q Consensus 252 C~~c~~ 257 (380)
|.+|..
T Consensus 95 CsaC~~ 100 (383)
T KOG4577|consen 95 CSACQE 100 (383)
T ss_pred chhhcC
Confidence 999993
No 16
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=97.45 E-value=3.2e-05 Score=71.73 Aligned_cols=64 Identities=19% Similarity=0.444 Sum_probs=57.0
Q ss_pred CCCCCCccccCCcccccCceEeeCCceecCCCcccCCCCCCCCCceeeccCCcccccccccccc
Q 016954 109 FPEGYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREHY 172 (380)
Q Consensus 109 ~~~~~~~C~~C~~~I~~g~~v~alg~~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~cy~~~f 172 (380)
+......|.+|.+.+++.+.+...+..||..||+|..|+..|+...+....|.+||+..+.+++
T Consensus 104 ~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~ 167 (200)
T KOG1700|consen 104 FAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLF 167 (200)
T ss_pred hhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheee
Confidence 3446788999999999889999999999999999999999999999999999999987766543
No 17
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=97.32 E-value=2.5e-05 Score=71.50 Aligned_cols=59 Identities=22% Similarity=0.598 Sum_probs=54.3
Q ss_pred CccccCCcccccCceEeeCCceecCCCcccCCCCCCCCCceeeccCCcccccccccccc
Q 016954 114 RICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREHY 172 (380)
Q Consensus 114 ~~C~~C~~~I~~g~~v~alg~~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~cy~~~f 172 (380)
..|..|++.+++-+.|+++++.||..||+|..|+.+|....|--.+.++||..+|.+..
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~ 63 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQV 63 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccce
Confidence 56889999999889999999999999999999999999888887899999999998764
No 18
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=97.20 E-value=0.00027 Score=47.00 Aligned_cols=37 Identities=19% Similarity=0.325 Sum_probs=28.4
Q ss_pred cccccCCcccCCCCcceEEecccccccccCCCCccCCCCcccccCCcC
Q 016954 175 KCDVCKHFIPSNHGGLIEYRAHPFWVQKYCPSHEHDGTPRCCSCERME 222 (380)
Q Consensus 175 kC~~C~~~I~~~~~~~i~~~~~~fw~qkycp~h~H~~CF~C~~C~r~l 222 (380)
+|..|++.|.+.. ..+.+.+ ..||..||+|..|+++|
T Consensus 1 ~C~~C~~~i~~~~-~~~~~~~----------~~~H~~Cf~C~~C~~~L 37 (39)
T smart00132 1 KCAGCGKPIRGGE-LVLRALG----------KVWHPECFKCSKCGKPL 37 (39)
T ss_pred CccccCCcccCCc-EEEEeCC----------ccccccCCCCcccCCcC
Confidence 5899999998752 2444444 34799999999999877
No 19
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=96.98 E-value=0.00012 Score=68.38 Aligned_cols=114 Identities=23% Similarity=0.456 Sum_probs=87.9
Q ss_pred cCCcccccCceEeeCCceecCCCcccCCCCCCCC--CceeeccCCcccccccccc--cccccccccCCcccCCCCcceEE
Q 016954 118 GCNNEIGHGRFLNCLDVFWHPECFCCHACHQPIT--DIEFSTSENRPYHKSCYRE--HYHPKCDVCKHFIPSNHGGLIEY 193 (380)
Q Consensus 118 ~C~~~I~~g~~v~alg~~wH~~CF~C~~C~~~L~--~~~f~~~dg~~YC~~cy~~--~f~pkC~~C~~~I~~~~~~~i~~ 193 (380)
+|+..|.+.-.+.+.+..||..|..|..|...+. ...|.. +|..||..+|.. .+..+|..|...|...+ .+
T Consensus 1 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~--~l-- 75 (235)
T KOG0490|consen 1 GCGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTISQLD--EL-- 75 (235)
T ss_pred CCCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCcCHHH--HH--
Confidence 3677774444456779999999999999999998 667777 999999999998 78889999999996432 22
Q ss_pred ecccccccccCCCCccCCCCcccccCCcCCCCCceEEccCCcccChhhhhh
Q 016954 194 RAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAYVALDDGRKLCLECLDS 244 (380)
Q Consensus 194 ~~~~fw~qkycp~h~H~~CF~C~~C~r~l~~g~~f~~l~dg~~~C~~C~~~ 244 (380)
.+.| ... |--||.|..|.+.+..++.+.+.......|...+..
T Consensus 76 -er~f------~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~ 118 (235)
T KOG0490|consen 76 -ERAF------EKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKE 118 (235)
T ss_pred -HHhh------cCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhh
Confidence 2222 122 778999999998887777777555558888888765
No 20
>PF14891 Peptidase_M91: Effector protein
Probab=86.50 E-value=0.42 Score=43.21 Aligned_cols=17 Identities=29% Similarity=0.598 Sum_probs=15.6
Q ss_pred hhHHHHHhHHHHhhhcC
Q 016954 358 GTILAHEMMHGWMRLQG 374 (380)
Q Consensus 358 g~ilahe~~ha~l~l~g 374 (380)
-.+|||||.|||=.++|
T Consensus 104 ~v~L~HEL~HA~~~~~G 120 (174)
T PF14891_consen 104 FVVLYHELIHAYDYMNG 120 (174)
T ss_pred HHHHHHHHHHHHHHHCC
Confidence 37899999999999998
No 21
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=86.42 E-value=0.4 Score=37.89 Aligned_cols=19 Identities=32% Similarity=0.406 Sum_probs=15.3
Q ss_pred hhhhHHHHHhHHHHhhhcC
Q 016954 356 LTGTILAHEMMHGWMRLQG 374 (380)
Q Consensus 356 ~~g~ilahe~~ha~l~l~g 374 (380)
-.-.+||||++|++..-.|
T Consensus 60 ~~~~llaHEl~Hv~Qq~~g 78 (79)
T PF13699_consen 60 EGRALLAHELAHVVQQRRG 78 (79)
T ss_pred CcchhHhHHHHHHHhhccC
Confidence 3457999999999987655
No 22
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=82.75 E-value=1.5 Score=35.82 Aligned_cols=24 Identities=29% Similarity=0.455 Sum_probs=18.2
Q ss_pred cCCChhhhhhHHHHHhHHHHhhhc
Q 016954 350 YGLPRLLTGTILAHEMMHGWMRLQ 373 (380)
Q Consensus 350 ~glp~~~~g~ilahe~~ha~l~l~ 373 (380)
.+-+......+|+||++|+|+...
T Consensus 18 ~~~~~~~~~~~l~HE~~H~~~~~~ 41 (128)
T PF13485_consen 18 QGSDEDWLDRVLAHELAHQWFGNY 41 (128)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHH
Confidence 445555555999999999998765
No 23
>smart00726 UIM Ubiquitin-interacting motif. Present in proteasome subunit S5a and other ubiquitin-associated proteins.
Probab=81.27 E-value=1.2 Score=27.70 Aligned_cols=21 Identities=38% Similarity=0.569 Sum_probs=15.8
Q ss_pred CcchHHHHHHHhchhhhhhcC
Q 016954 43 QENEDIDRAIALSLLEENQKG 63 (380)
Q Consensus 43 ~~~e~~~~aia~sl~e~~~~~ 63 (380)
.++|+|.+||++|+.|.+...
T Consensus 1 ~EDe~Lq~Ai~lSl~e~e~~~ 21 (26)
T smart00726 1 DEDEDLQLALELSLQEAEESX 21 (26)
T ss_pred ChHHHHHHHHHHhHHHhhhcc
Confidence 367889999999987765543
No 24
>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=80.81 E-value=1.1 Score=39.29 Aligned_cols=22 Identities=27% Similarity=0.132 Sum_probs=19.1
Q ss_pred CChhhhhhHHHHHhHHHHhhhc
Q 016954 352 LPRLLTGTILAHEMMHGWMRLQ 373 (380)
Q Consensus 352 lp~~~~g~ilahe~~ha~l~l~ 373 (380)
.|....-.+|+|||.|||+.+.
T Consensus 55 ~~~~~~~~tL~HEm~H~~~~~~ 76 (157)
T PF10263_consen 55 NPEEELIDTLLHEMAHAAAYVF 76 (157)
T ss_pred hHHHHHHHHHHHHHHHHHhhhc
Confidence 5667778899999999999877
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=79.88 E-value=2.1 Score=34.64 Aligned_cols=31 Identities=26% Similarity=0.176 Sum_probs=24.8
Q ss_pred EEEEEecCCChhhhhhHHHHHhHHHHhhhcC
Q 016954 344 TAILILYGLPRLLTGTILAHEMMHGWMRLQG 374 (380)
Q Consensus 344 ~~il~l~glp~~~~g~ilahe~~ha~l~l~g 374 (380)
.-|+|=..++..-.-.+||||++|.++.-.+
T Consensus 29 ~~I~in~~~~~~~~~f~laHELgH~~~~~~~ 59 (122)
T PF06114_consen 29 PIIFINSNLSPERQRFTLAHELGHILLHHGD 59 (122)
T ss_dssp TEEEEESSS-HHHHHHHHHHHHHHHHHHH-H
T ss_pred CEEEECCCCCHHHHHHHHHHHHHHHHhhhcc
Confidence 4578888899999999999999999986543
No 26
>PF02809 UIM: Ubiquitin interaction motif; InterPro: IPR003903 The Ubiquitin Interacting Motif (UIM), or 'LALAL-motif', is a stretch of about 20 amino acid residues, which was first described in the 26S proteasome subunit PSD4/RPN-10 that is known to recognise ubiquitin [,]. In addition, the UIM is found, often in tandem or triplet arrays, in a variety of proteins either involved in ubiquitination and ubiquitin metabolism, or known to interact with ubiquitin-like modifiers. Among the UIM proteins are two different subgroups of the UBP (ubiquitin carboxy-terminal hydrolase) family of deubiquitinating enzymes, one F-box protein, one family of HECT-containing ubiquitin-ligases (E3s) from plants, and several proteins containing ubiquitin-associated UBA and/or UBX domains []. In most of these proteins, the UIM occurs in multiple copies and in association with other domains such as UBA (IPR015940 from INTERPRO), UBX (IPR001012 from INTERPRO), ENTH, EH (IPR000261 from INTERPRO), VHS (IPR002014 from INTERPRO), SH3 (IPR001452 from INTERPRO), HECT (IPR000569 from INTERPRO), VWFA (IPR002035 from INTERPRO), EF-hand calcium-binding, WD-40 (IPR001680 from INTERPRO), F-box (IPR001810 from INTERPRO), LIM (IPR001781 from INTERPRO), protein kinase (IPR000719 from INTERPRO), ankyrin (IPR002110 from INTERPRO), PX (IPR001683 from INTERPRO), phosphatidylinositol 3- and 4-kinase (IPR000403 from INTERPRO), C2 (IPR000008 from INTERPRO), OTU (IPR003323 from INTERPRO), dnaJ (IPR001623 from INTERPRO), RING-finger (IPR001841 from INTERPRO) or FYVE-finger (IPR017455 from INTERPRO). UIMs have been shown to bind ubiquitin and to serve as a specific targeting signal important for monoubiquitination. Thus, UIMs may have several functions in ubiquitin metabolism each of which may require different numbers of UIMs [, , ]. The UIM is unlikely to form an independent folding domain. Instead, based on the spacing of the conserved residues, the motif probably forms a short alpha-helix that can be embedded into different protein folds []. Some proteins known to contain an UIM are listed below: Eukaryotic PSD4/RPN-10/S5, a multi-ubiquitin binding subunit of the 26S proteasome. Vertebrate Machado-Joseph disease protein 1 (Ataxin-3), which acts as a histone-binding protein that regulates transcription; defects in Ataxin-3 cause the neurodegenerative disorder Machado-Joseph disease (MJD). Vertebrate epsin and epsin2. Vertebrate hepatocyte growth factor-regulated tyrosine kinase substrate (HRS). Mammalian epidermal growth factor receptor substrate 15 (EPS15), which is involved in cell growth regulation. Mammalian epidermal growth factor receptor substrate EPS15R. Drosophila melanogaster (Fruit fly) liquid facets (lqf), an epsin. Yeast VPS27 vacuolar sorting protein, which is required for membrane traffic to the vacuole. ; PDB: 2KDE_A 2KDF_A 1YX6_A 1YX5_A 1YX4_A 1P9C_A 1UEL_B 1P9D_S 2KLZ_A.
Probab=78.57 E-value=1 Score=25.59 Aligned_cols=16 Identities=50% Similarity=0.800 Sum_probs=12.1
Q ss_pred CcchHHHHHHHhchhh
Q 016954 43 QENEDIDRAIALSLLE 58 (380)
Q Consensus 43 ~~~e~~~~aia~sl~e 58 (380)
.|+++|.+||++|+.|
T Consensus 2 ~Ed~~L~~Al~~S~~e 17 (18)
T PF02809_consen 2 DEDEDLQRALEMSLEE 17 (18)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred chHHHHHHHHHhhhcc
Confidence 4667888888888764
No 27
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=73.34 E-value=2.5 Score=36.97 Aligned_cols=22 Identities=32% Similarity=0.306 Sum_probs=16.8
Q ss_pred ChhhhhhHHHHHhHHHHhhhcC
Q 016954 353 PRLLTGTILAHEMMHGWMRLQG 374 (380)
Q Consensus 353 p~~~~g~ilahe~~ha~l~l~g 374 (380)
|....-.||+|||.|+|+.+.|
T Consensus 55 ~~~~l~~~l~HEm~H~~~~~~g 76 (146)
T smart00731 55 GRDRLRETLLHELCHAALYLFG 76 (146)
T ss_pred cHHHHHhhHHHHHHHHHHHHhC
Confidence 3445567999999999998653
No 28
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=70.13 E-value=2.2 Score=38.78 Aligned_cols=50 Identities=24% Similarity=0.537 Sum_probs=38.0
Q ss_pred cCCCCcccccCCcCCCCCceEEccCCcccChhhhhhhccCCCCCCcchHHH
Q 016954 209 HDGTPRCCSCERMEPQDTAYVALDDGRKLCLECLDSAIMDTNECQPLYLDI 259 (380)
Q Consensus 209 H~~CF~C~~C~r~l~~g~~f~~l~dg~~~C~~C~~~~v~~~~~C~~c~~~I 259 (380)
-..||+|-.|=.....-..+ .-+=|+++|.+|...++..+..|.-|.+.|
T Consensus 128 ~~~~~~CPiCl~~~sek~~v-sTkCGHvFC~~Cik~alk~~~~CP~C~kkI 177 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPV-STKCGHVFCSQCIKDALKNTNKCPTCRKKI 177 (187)
T ss_pred cccccCCCceecchhhcccc-ccccchhHHHHHHHHHHHhCCCCCCccccc
Confidence 34678898886444322233 236799999999999999999999999777
No 29
>PHA02456 zinc metallopeptidase motif-containing protein
Probab=68.34 E-value=2.8 Score=35.33 Aligned_cols=15 Identities=40% Similarity=0.674 Sum_probs=12.3
Q ss_pred hHHHHHhHHHHhhhc
Q 016954 359 TILAHEMMHGWMRLQ 373 (380)
Q Consensus 359 ~ilahe~~ha~l~l~ 373 (380)
..||||+.|+|+.-.
T Consensus 81 ~TL~HEL~H~WQ~Rs 95 (141)
T PHA02456 81 DTLAHELNHAWQFRT 95 (141)
T ss_pred HHHHHHHHHHHhhhc
Confidence 569999999998543
No 30
>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=68.21 E-value=3 Score=37.01 Aligned_cols=13 Identities=38% Similarity=0.618 Sum_probs=10.9
Q ss_pred hhHHHHHhHHHHh
Q 016954 358 GTILAHEMMHGWM 370 (380)
Q Consensus 358 g~ilahe~~ha~l 370 (380)
=-|+||||+|+..
T Consensus 136 lDVvaHEltHGVt 148 (150)
T PF01447_consen 136 LDVVAHELTHGVT 148 (150)
T ss_dssp HHHHHHHHHHHHH
T ss_pred cceeeeccccccc
Confidence 3689999999864
No 31
>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=67.09 E-value=3 Score=37.89 Aligned_cols=19 Identities=21% Similarity=0.329 Sum_probs=14.5
Q ss_pred hhhhhHHHHHhHHHHhhhc
Q 016954 355 LLTGTILAHEMMHGWMRLQ 373 (380)
Q Consensus 355 ~~~g~ilahe~~ha~l~l~ 373 (380)
.....+|+|||.|||=.+.
T Consensus 69 ~~l~~~l~HELIHayD~cr 87 (173)
T PF09768_consen 69 GHLEDTLTHELIHAYDHCR 87 (173)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 3445899999999995544
No 32
>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=66.97 E-value=3.4 Score=39.38 Aligned_cols=20 Identities=35% Similarity=0.702 Sum_probs=16.2
Q ss_pred cC--CChhhhhhHHHHHhHHHH
Q 016954 350 YG--LPRLLTGTILAHEMMHGW 369 (380)
Q Consensus 350 ~g--lp~~~~g~ilahe~~ha~ 369 (380)
|| +|...+..++||||+|.|
T Consensus 158 ~~~~~~~~~~a~t~AHElGHnl 179 (244)
T cd04270 158 YGKRVPTKESDLVTAHELGHNF 179 (244)
T ss_pred cCCccchhHHHHHHHHHHHHhc
Confidence 55 466778899999999986
No 33
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=65.82 E-value=3.8 Score=40.92 Aligned_cols=73 Identities=22% Similarity=0.367 Sum_probs=43.8
Q ss_pred CCccccCCcccccCceEeeCCceecCCCcccCCCCCCCCCceeeccCCccccccccccc--------ccccccccCCccc
Q 016954 113 YRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREH--------YHPKCDVCKHFIP 184 (380)
Q Consensus 113 ~~~C~~C~~~I~~g~~v~alg~~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~cy~~~--------f~pkC~~C~~~I~ 184 (380)
...|.+|++.-. -..|++|-.|. +--+|..||... -+|.|..|...-.
T Consensus 8 ~v~CdgC~k~~~------------t~rrYkCL~C~------------DyDlC~sCyen~~tt~~H~~dHPmqcil~~~df 63 (381)
T KOG1280|consen 8 GVSCDGCGKTAF------------TFRRYKCLRCS------------DYDLCFSCYENGATTPIHDEDHPMQCILSRVDF 63 (381)
T ss_pred Cceeccccccce------------eeeeeEeeeec------------chhHHHHHhhcCCCCcccCCCCceeEEeeccce
Confidence 356888887653 22355555552 123577777643 2455665544322
Q ss_pred CCCCcceEEecccccccccCCCCccCCCCcccccCCc
Q 016954 185 SNHGGLIEYRAHPFWVQKYCPSHEHDGTPRCCSCERM 221 (380)
Q Consensus 185 ~~~~~~i~~~~~~fw~qkycp~h~H~~CF~C~~C~r~ 221 (380)
-+.|.+.++ +||-+.||+|-.|++.
T Consensus 64 -----eL~f~Ge~i-------~~y~~qSftCPyC~~~ 88 (381)
T KOG1280|consen 64 -----ELYFGGEPI-------SHYDPQSFTCPYCGIM 88 (381)
T ss_pred -----eeEecCccc-------cccccccccCCccccc
Confidence 144555544 5777889999999975
No 34
>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=64.89 E-value=3.5 Score=38.49 Aligned_cols=15 Identities=40% Similarity=0.663 Sum_probs=12.5
Q ss_pred hhhHHHHHhHHHHhh
Q 016954 357 TGTILAHEMMHGWMR 371 (380)
Q Consensus 357 ~g~ilahe~~ha~l~ 371 (380)
.-.||-|||||+|+-
T Consensus 96 i~Gvl~HE~~H~~Q~ 110 (205)
T PF04450_consen 96 IIGVLYHEMVHCWQW 110 (205)
T ss_pred HHHHHHHHHHHHhhc
Confidence 346899999999984
No 35
>PRK14873 primosome assembly protein PriA; Provisional
Probab=63.92 E-value=5.2 Score=43.80 Aligned_cols=49 Identities=22% Similarity=0.523 Sum_probs=35.7
Q ss_pred CCccccCCcccccCceEeeCCceecCCCcccCCCCCCCCCceeeccCCcccccccccccccccccccCCc
Q 016954 113 YRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREHYHPKCDVCKHF 182 (380)
Q Consensus 113 ~~~C~~C~~~I~~g~~v~alg~~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~cy~~~f~pkC~~C~~~ 182 (380)
.-.|..|+..+ +|..|+.+|. |...++.+.|.-|-......+|..|+..
T Consensus 383 ~l~C~~Cg~~~------------------~C~~C~~~L~---~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 383 SLACARCRTPA------------------RCRHCTGPLG---LPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred eeEhhhCcCee------------------ECCCCCCcee---EecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 35677777665 6888888774 4445677889999665556689999875
No 36
>PF12773 DZR: Double zinc ribbon
Probab=63.92 E-value=6.1 Score=27.77 Aligned_cols=20 Identities=20% Similarity=0.511 Sum_probs=9.5
Q ss_pred cccChhhhhhhccCCCCCCc
Q 016954 235 RKLCLECLDSAIMDTNECQP 254 (380)
Q Consensus 235 ~~~C~~C~~~~v~~~~~C~~ 254 (380)
..+|..|...+-.+...|..
T Consensus 29 ~~~C~~Cg~~~~~~~~fC~~ 48 (50)
T PF12773_consen 29 KKICPNCGAENPPNAKFCPN 48 (50)
T ss_pred CCCCcCCcCCCcCCcCccCc
Confidence 44555555544334444443
No 37
>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=63.01 E-value=7.4 Score=35.43 Aligned_cols=25 Identities=28% Similarity=0.258 Sum_probs=19.5
Q ss_pred EEEEEecCCChhhhhhHHHHHhHHH
Q 016954 344 TAILILYGLPRLLTGTILAHEMMHG 368 (380)
Q Consensus 344 ~~il~l~glp~~~~g~ilahe~~ha 368 (380)
-+|....+-.-+.++.++|||++|.
T Consensus 118 ~~i~~~~~~~~~~~a~~~AHelGH~ 142 (199)
T PF01421_consen 118 CGIVEDHSRSGLSFAVIIAHELGHN 142 (199)
T ss_dssp EEEEE-SSSSHHHHHHHHHHHHHHH
T ss_pred CcEeeeccchhHHHHHHHHHHHHHh
Confidence 4555666677888999999999995
No 38
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=62.70 E-value=7.6 Score=36.48 Aligned_cols=30 Identities=23% Similarity=0.158 Sum_probs=23.8
Q ss_pred EEEEEecCCChhhhhhHHHHHhHHHHhhhc
Q 016954 344 TAILILYGLPRLLTGTILAHEMMHGWMRLQ 373 (380)
Q Consensus 344 ~~il~l~glp~~~~g~ilahe~~ha~l~l~ 373 (380)
.-|++---++...---+||||++|+||--.
T Consensus 59 ~~I~iN~n~~~~r~rFtlAHELGH~llH~~ 88 (213)
T COG2856 59 PVIYINANNSLERKRFTLAHELGHALLHTD 88 (213)
T ss_pred ceEEEeCCCCHHHHHHHHHHHHhHHHhccc
Confidence 467777777777777899999999998543
No 39
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=61.84 E-value=9.9 Score=26.11 Aligned_cols=42 Identities=17% Similarity=0.305 Sum_probs=29.5
Q ss_pred ccccCCcCCCCCceEEccCCcccChhhhhhhccCCCCCCcch
Q 016954 215 CCSCERMEPQDTAYVALDDGRKLCLECLDSAIMDTNECQPLY 256 (380)
Q Consensus 215 C~~C~r~l~~g~~f~~l~dg~~~C~~C~~~~v~~~~~C~~c~ 256 (380)
|..|.+......+++.+.=|..+|..|...+......|.-|.
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~ 43 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICR 43 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCC
Confidence 667776664455677788899999999998653345565554
No 40
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=60.88 E-value=6.1 Score=28.55 Aligned_cols=30 Identities=23% Similarity=0.678 Sum_probs=22.1
Q ss_pred cccccCCcCCCCCceEEccCCcccChhhhhhh
Q 016954 214 RCCSCERMEPQDTAYVALDDGRKLCLECLDSA 245 (380)
Q Consensus 214 ~C~~C~r~l~~g~~f~~l~dg~~~C~~C~~~~ 245 (380)
.|..|+..+..-.++ .+.|| .+|..|+.++
T Consensus 1 ~C~iCg~kigl~~~~-k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRF-KIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccce-eccCc-cchHHHHHHh
Confidence 488898776544443 37788 6999999885
No 41
>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=60.58 E-value=5.4 Score=36.02 Aligned_cols=24 Identities=33% Similarity=0.394 Sum_probs=17.2
Q ss_pred EEEEecCCChhhhhhHHHHHhHHHH
Q 016954 345 AILILYGLPRLLTGTILAHEMMHGW 369 (380)
Q Consensus 345 ~il~l~glp~~~~g~ilahe~~ha~ 369 (380)
+|....+ +.+..+.++|||++|.+
T Consensus 122 ~v~~~~~-~~~~~~~~~aHElGH~l 145 (192)
T cd04267 122 GVVEDTG-FTLLTALTMAHELGHNL 145 (192)
T ss_pred EEEecCC-cceeehhhhhhhHHhhc
Confidence 4444444 36778899999999965
No 42
>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=59.18 E-value=7.6 Score=41.05 Aligned_cols=38 Identities=18% Similarity=0.538 Sum_probs=27.7
Q ss_pred ccCCCCCCCCCceeeccCCccccccccccc-ccccccccCCc
Q 016954 142 CCHACHQPITDIEFSTSENRPYHKSCYREH-YHPKCDVCKHF 182 (380)
Q Consensus 142 ~C~~C~~~L~~~~f~~~dg~~YC~~cy~~~-f~pkC~~C~~~ 182 (380)
+|..|+.+| .|...++.+.|..|-... ....|..|+..
T Consensus 224 ~C~~C~~~l---~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 224 CCPNCDVSL---TYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred CCCCCCCce---EEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 677787776 455567888899886543 45689999874
No 43
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=58.74 E-value=11 Score=28.69 Aligned_cols=47 Identities=17% Similarity=0.367 Sum_probs=21.9
Q ss_pred cccCCCCCCCCCceeeccCCcccccccccccccccccccCCcccCCC
Q 016954 141 FCCHACHQPITDIEFSTSENRPYHKSCYREHYHPKCDVCKHFIPSNH 187 (380)
Q Consensus 141 F~C~~C~~~L~~~~f~~~dg~~YC~~cy~~~f~pkC~~C~~~I~~~~ 187 (380)
.+|+.|..-|...--...=...||..|-...++..|.+|+.+-...+
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~qD 54 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQD 54 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-SS
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHHHH
Confidence 45666666554432222334578888888888889999999876554
No 44
>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=58.50 E-value=7.4 Score=35.55 Aligned_cols=27 Identities=33% Similarity=0.363 Sum_probs=18.5
Q ss_pred EEEEecC----CChhhhhhHHHHHhHHHHhh
Q 016954 345 AILILYG----LPRLLTGTILAHEMMHGWMR 371 (380)
Q Consensus 345 ~il~l~g----lp~~~~g~ilahe~~ha~l~ 371 (380)
.|+|-.| |...-.-+|||||++|...+
T Consensus 73 ~I~v~~~ll~~~~~~el~aVlaHElgH~~~~ 103 (226)
T PF01435_consen 73 RIVVTSGLLESLSEDELAAVLAHELGHIKHR 103 (226)
T ss_dssp EEEEEHHHHHHSSHHHHHHHHHHHHHHHHTT
T ss_pred EEEEeChhhhcccHHHHHHHHHHHHHHHHcC
Confidence 3444444 45555568999999998765
No 45
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=56.31 E-value=9.7 Score=27.68 Aligned_cols=44 Identities=7% Similarity=0.014 Sum_probs=32.1
Q ss_pred CcccccCCcCCCCCceEEccCCcccChhhhhhhccCCCCCCcchHHH
Q 016954 213 PRCCSCERMEPQDTAYVALDDGRKLCLECLDSAIMDTNECQPLYLDI 259 (380)
Q Consensus 213 F~C~~C~r~l~~g~~f~~l~dg~~~C~~C~~~~v~~~~~C~~c~~~I 259 (380)
|.|..|+..+. ... ....|+.||+.|..+.+.....|--|..++
T Consensus 2 ~~Cpi~~~~~~--~Pv-~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~ 45 (63)
T smart00504 2 FLCPISLEVMK--DPV-ILPSGQTYERRAIEKWLLSHGTDPVTGQPL 45 (63)
T ss_pred cCCcCCCCcCC--CCE-ECCCCCEEeHHHHHHHHHHCCCCCCCcCCC
Confidence 57999998763 354 467899999999998776656666666443
No 46
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=55.99 E-value=7.4 Score=31.40 Aligned_cols=13 Identities=31% Similarity=0.713 Sum_probs=8.1
Q ss_pred cccccccCCcccC
Q 016954 173 HPKCDVCKHFIPS 185 (380)
Q Consensus 173 ~pkC~~C~~~I~~ 185 (380)
...|.+|++.|..
T Consensus 78 ~~~C~vC~k~l~~ 90 (109)
T PF10367_consen 78 STKCSVCGKPLGN 90 (109)
T ss_pred CCCccCcCCcCCC
Confidence 3467777776654
No 47
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=55.59 E-value=11 Score=41.07 Aligned_cols=9 Identities=44% Similarity=0.914 Sum_probs=5.2
Q ss_pred ccccCCccc
Q 016954 115 ICAGCNNEI 123 (380)
Q Consensus 115 ~C~~C~~~I 123 (380)
+|..|+..+
T Consensus 3 ~Cp~Cg~~n 11 (645)
T PRK14559 3 ICPQCQFEN 11 (645)
T ss_pred cCCCCCCcC
Confidence 466666555
No 48
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=54.37 E-value=6.7 Score=34.96 Aligned_cols=55 Identities=16% Similarity=0.363 Sum_probs=36.7
Q ss_pred cccccccccccccccccccCCcccCCC--CcceEEecccccccccCCCCccCCCCcccccCCcCCCCCce
Q 016954 161 RPYHKSCYREHYHPKCDVCKHFIPSNH--GGLIEYRAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAY 228 (380)
Q Consensus 161 ~~YC~~cy~~~f~pkC~~C~~~I~~~~--~~~i~~~~~~fw~qkycp~h~H~~CF~C~~C~r~l~~g~~f 228 (380)
.-||..|-.+. -..|..|+.+|.+.. .|++.+.. ||+.-- -|..||++.|.....
T Consensus 28 ~~fC~kCG~~t-I~~Cp~C~~~IrG~y~v~gv~~~g~-----------~~~~Ps-YC~~CGkpyPWt~~~ 84 (158)
T PF10083_consen 28 EKFCSKCGAKT-ITSCPNCSTPIRGDYHVEGVFGLGG-----------HYEAPS-YCHNCGKPYPWTENA 84 (158)
T ss_pred HHHHHHhhHHH-HHHCcCCCCCCCCceecCCeeeeCC-----------CCCCCh-hHHhCCCCCchHHHH
Confidence 45899997665 568999999999863 23444422 233221 399999999865543
No 49
>PF04228 Zn_peptidase: Putative neutral zinc metallopeptidase; InterPro: IPR007343 Members of this family of bacterial proteins are described as hypothetical proteins or zinc metallopeptidases. The majority have a HExxH zinc-binding motif characteristic of neutral zinc metallopeptidases, however there is no evidence to support their function as metallopeptidases.
Probab=53.61 E-value=9.1 Score=37.69 Aligned_cols=22 Identities=32% Similarity=0.365 Sum_probs=17.9
Q ss_pred hhhhhhHHHHHhHHHHhhhcCC
Q 016954 354 RLLTGTILAHEMMHGWMRLQGA 375 (380)
Q Consensus 354 ~~~~g~ilahe~~ha~l~l~g~ 375 (380)
.+.--+|||||+.|.-+.|.|.
T Consensus 167 ~~a~ayVlAHEyGHHVQ~l~Gi 188 (292)
T PF04228_consen 167 DFAQAYVLAHEYGHHVQNLLGI 188 (292)
T ss_pred HHHHHHHHHHHHHHHHHHHhhh
Confidence 3455679999999999998873
No 50
>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=53.44 E-value=8.1 Score=35.10 Aligned_cols=26 Identities=23% Similarity=0.174 Sum_probs=21.1
Q ss_pred EEEEEecCCChhhhhhHHHHHhHHHH
Q 016954 344 TAILILYGLPRLLTGTILAHEMMHGW 369 (380)
Q Consensus 344 ~~il~l~glp~~~~g~ilahe~~ha~ 369 (380)
+-=+-|.-+|.-+.-+|++||++|-.
T Consensus 151 ~ln~~L~~~P~~~idYVvvHEL~Hl~ 176 (205)
T PF01863_consen 151 TLNWRLVMAPPEVIDYVVVHELCHLR 176 (205)
T ss_pred EeecccccCCccHHHHHHHHHHHHhc
Confidence 33355667999999999999999973
No 51
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=52.92 E-value=4.5 Score=33.48 Aligned_cols=29 Identities=28% Similarity=0.419 Sum_probs=17.8
Q ss_pred ccccCCcccccCceEeeC-CceecCCCccc
Q 016954 115 ICAGCNNEIGHGRFLNCL-DVFWHPECFCC 143 (380)
Q Consensus 115 ~C~~C~~~I~~g~~v~al-g~~wH~~CF~C 143 (380)
.|..|+++|+.|+.+++. +..-|-.||+=
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~ 33 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFRE 33 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHH
Confidence 577777777667666553 34556666543
No 52
>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=52.79 E-value=6.7 Score=33.47 Aligned_cols=9 Identities=44% Similarity=0.730 Sum_probs=8.7
Q ss_pred HHHHHhHHH
Q 016954 360 ILAHEMMHG 368 (380)
Q Consensus 360 ilahe~~ha 368 (380)
+++||+|||
T Consensus 89 ~~~HEigHa 97 (140)
T smart00235 89 VAAHELGHA 97 (140)
T ss_pred cHHHHHHHH
Confidence 899999999
No 53
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=52.77 E-value=9.8 Score=38.83 Aligned_cols=26 Identities=42% Similarity=0.542 Sum_probs=22.4
Q ss_pred CCCCcchHHHHHHHhchhhhhhcCCC
Q 016954 40 PLEQENEDIDRAIALSLLEENQKGEN 65 (380)
Q Consensus 40 ~~~~~~e~~~~aia~sl~e~~~~~~~ 65 (380)
.+.+|+|||..||++||.|.++.+|.
T Consensus 161 ~~k~EeEdiaKAi~lSL~E~~~Q~k~ 186 (462)
T KOG2199|consen 161 SSKQEEEDIAKAIELSLKEQEKQKKL 186 (462)
T ss_pred cccccHHHHHHHHHhhHHHHhhchhh
Confidence 45789999999999999998887665
No 54
>PRK04351 hypothetical protein; Provisional
Probab=52.60 E-value=11 Score=33.50 Aligned_cols=18 Identities=33% Similarity=0.517 Sum_probs=15.2
Q ss_pred hhhHHHHHhHHHHhhhcC
Q 016954 357 TGTILAHEMMHGWMRLQG 374 (380)
Q Consensus 357 ~g~ilahe~~ha~l~l~g 374 (380)
.-.||+|||.|.++-+.|
T Consensus 61 l~~vv~HElcH~~~~~~g 78 (149)
T PRK04351 61 LIGIIKHELCHYHLHLEG 78 (149)
T ss_pred HHhhHHHHHHHHHHHHHC
Confidence 358999999999988865
No 55
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=52.51 E-value=13 Score=29.90 Aligned_cols=30 Identities=20% Similarity=0.434 Sum_probs=21.5
Q ss_pred CCccccCCcccccCceEee-CCceecCCCcc
Q 016954 113 YRICAGCNNEIGHGRFLNC-LDVFWHPECFC 142 (380)
Q Consensus 113 ~~~C~~C~~~I~~g~~v~a-lg~~wH~~CF~ 142 (380)
...|..|+++|+.+.++.. .|..+|..|++
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 4679999999976555443 46678888763
No 56
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=51.77 E-value=7.8 Score=30.76 Aligned_cols=31 Identities=26% Similarity=0.528 Sum_probs=22.8
Q ss_pred cccccCCcCCCCCceEEccCCc---ccChhhhhh
Q 016954 214 RCCSCERMEPQDTAYVALDDGR---KLCLECLDS 244 (380)
Q Consensus 214 ~C~~C~r~l~~g~~f~~l~dg~---~~C~~C~~~ 244 (380)
.|.+||.|+.....+....||. -||.-||..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 4899999987655455555664 599999985
No 57
>PRK04860 hypothetical protein; Provisional
Probab=51.19 E-value=11 Score=33.89 Aligned_cols=21 Identities=14% Similarity=0.254 Sum_probs=16.9
Q ss_pred ChhhhhhHHHHHhHHHHhhhc
Q 016954 353 PRLLTGTILAHEMMHGWMRLQ 373 (380)
Q Consensus 353 p~~~~g~ilahe~~ha~l~l~ 373 (380)
+...+-.|++|||.|.|+-+.
T Consensus 59 ~~~~l~~~v~HEl~H~~~~~~ 79 (160)
T PRK04860 59 QQAFIDEVVPHELAHLLVYQL 79 (160)
T ss_pred cHHHHHhHHHHHHHHHHHHHH
Confidence 334456899999999999977
No 58
>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=50.95 E-value=9.9 Score=34.29 Aligned_cols=17 Identities=29% Similarity=0.419 Sum_probs=13.6
Q ss_pred ChhhhhhHHHHHhHHHH
Q 016954 353 PRLLTGTILAHEMMHGW 369 (380)
Q Consensus 353 p~~~~g~ilahe~~ha~ 369 (380)
|......++|||++|.|
T Consensus 138 ~~~~~~~~~AHEiGH~l 154 (196)
T PF13688_consen 138 PTYNGAITFAHEIGHNL 154 (196)
T ss_dssp -HHHHHHHHHHHHHHHT
T ss_pred CCCceehhhHHhHHHhc
Confidence 45677788999999986
No 59
>COG2738 Predicted Zn-dependent protease [General function prediction only]
Probab=50.63 E-value=8.4 Score=35.74 Aligned_cols=29 Identities=24% Similarity=0.225 Sum_probs=23.9
Q ss_pred cCCChhhhhhHHHHHhHHHHhhhcCCCCC
Q 016954 350 YGLPRLLTGTILAHEMMHGWMRLQGAFCL 378 (380)
Q Consensus 350 ~glp~~~~g~ilahe~~ha~l~l~g~~~l 378 (380)
|+=|....-+|.|||.+||.+-..+|+-|
T Consensus 85 y~g~Sia~~aVAAHEVGHAiQd~~~Y~~L 113 (226)
T COG2738 85 YYGPSIAAIAVAAHEVGHAIQDQEDYAFL 113 (226)
T ss_pred cCCccHHHHHHHHHHhhHHHhhhcccHHH
Confidence 56677788899999999999988887643
No 60
>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=50.32 E-value=8.9 Score=32.94 Aligned_cols=16 Identities=19% Similarity=0.164 Sum_probs=12.4
Q ss_pred ChhhhhhHHHHHhHHH
Q 016954 353 PRLLTGTILAHEMMHG 368 (380)
Q Consensus 353 p~~~~g~ilahe~~ha 368 (380)
+..-.-+|++||++||
T Consensus 101 ~~~~~~~v~~HEiGHa 116 (154)
T PF00413_consen 101 SGNDLQSVAIHEIGHA 116 (154)
T ss_dssp SSEEHHHHHHHHHHHH
T ss_pred hhhhhhhhhhhccccc
Confidence 3344568999999998
No 61
>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=50.02 E-value=11 Score=32.78 Aligned_cols=16 Identities=25% Similarity=0.285 Sum_probs=13.3
Q ss_pred hhhhhhHHHHHhHHHH
Q 016954 354 RLLTGTILAHEMMHGW 369 (380)
Q Consensus 354 ~~~~g~ilahe~~ha~ 369 (380)
...+..++|||++|+.
T Consensus 93 ~~~~~~~~~HElGH~L 108 (167)
T cd00203 93 TKEGAQTIAHELGHAL 108 (167)
T ss_pred cccchhhHHHHHHHHh
Confidence 3467899999999984
No 62
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=49.75 E-value=15 Score=27.53 Aligned_cols=27 Identities=26% Similarity=0.546 Sum_probs=15.7
Q ss_pred CCccccCCcccccCc-eEeeCCceecCCCcccCCCCCC
Q 016954 113 YRICAGCNNEIGHGR-FLNCLDVFWHPECFCCHACHQP 149 (380)
Q Consensus 113 ~~~C~~C~~~I~~g~-~v~alg~~wH~~CF~C~~C~~~ 149 (380)
.++|..|+..|...+ .+ =|.|..|+..
T Consensus 7 ~~~CtSCg~~i~~~~~~~----------~F~CPnCG~~ 34 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAV----------KFLCPNCGEV 34 (59)
T ss_pred CccccCCCCcccCCCccC----------EeeCCCCCCe
Confidence 456777777774333 22 1566666654
No 63
>PF04298 Zn_peptidase_2: Putative neutral zinc metallopeptidase; InterPro: IPR007395 Members of this family of bacterial proteins are described as hypothetical proteins or zinc-dependent proteases. The majority have a HExxH zinc-binding motif characteristic of neutral zinc metallopeptidases, however there is no evidence to support their function as metallopeptidases.
Probab=49.58 E-value=10 Score=35.82 Aligned_cols=26 Identities=23% Similarity=0.235 Sum_probs=20.7
Q ss_pred ChhhhhhHHHHHhHHHHhhhcCCCCC
Q 016954 353 PRLLTGTILAHEMMHGWMRLQGAFCL 378 (380)
Q Consensus 353 p~~~~g~ilahe~~ha~l~l~g~~~l 378 (380)
.-+..=+|.|||.+||-+.-+||.-|
T Consensus 85 ~SiaAvaVAAHEvGHAiQ~a~~Y~pl 110 (222)
T PF04298_consen 85 RSIAAVAVAAHEVGHAIQHAEGYAPL 110 (222)
T ss_pred CCHHHHHHHHHHHhHHHhccccCcHH
Confidence 34445589999999999999998644
No 64
>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=48.98 E-value=9.2 Score=33.32 Aligned_cols=13 Identities=23% Similarity=0.286 Sum_probs=10.9
Q ss_pred hhhHHHHHhHHHH
Q 016954 357 TGTILAHEMMHGW 369 (380)
Q Consensus 357 ~g~ilahe~~ha~ 369 (380)
.-.+++||++||-
T Consensus 94 ~~~~~~HEiGHaL 106 (165)
T cd04268 94 LRNTAEHELGHAL 106 (165)
T ss_pred HHHHHHHHHHHHh
Confidence 4588999999983
No 65
>KOG3624 consensus M13 family peptidase [Amino acid transport and metabolism]
Probab=48.73 E-value=8.4 Score=42.12 Aligned_cols=15 Identities=33% Similarity=0.654 Sum_probs=13.1
Q ss_pred hhhhhHHHHHhHHHH
Q 016954 355 LLTGTILAHEMMHGW 369 (380)
Q Consensus 355 ~~~g~ilahe~~ha~ 369 (380)
-..|.|||||++|++
T Consensus 516 g~iG~vigHEl~H~F 530 (687)
T KOG3624|consen 516 GGIGFVIGHELTHGF 530 (687)
T ss_pred HHHHHHHHHHHhhcc
Confidence 357999999999987
No 66
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=48.59 E-value=10 Score=25.34 Aligned_cols=24 Identities=21% Similarity=0.436 Sum_probs=17.0
Q ss_pred ccCCCCCCCCCceeeccCCccccccccc
Q 016954 142 CCHACHQPITDIEFSTSENRPYHKSCYR 169 (380)
Q Consensus 142 ~C~~C~~~L~~~~f~~~dg~~YC~~cy~ 169 (380)
.|..|+.. .|...||..||..|-.
T Consensus 10 ~C~~C~~~----~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 10 PCPVCGSR----WFYSDDGFYYCDRCGH 33 (36)
T ss_pred cCCCCCCe----EeEccCCEEEhhhCce
Confidence 46777643 5777899999977743
No 67
>PF05572 Peptidase_M43: Pregnancy-associated plasma protein-A; InterPro: IPR008754 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 M43 (cytophagalysin family, clan MA(M)), subfamily M43. The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The type example of this family is the pregnancy-associated plasma protein A (PAPP-A), which cleaves insulin-like growth factor (IGF) binding protein-4 (IGFBP-4), causing a dramatic reduction in its affinity for IGF-I and -II. Through this mechanism, PAPP-A is a regulator of IGF bioactivity in several systems, including the Homo sapiens ovary and the cardiovascular system [, , , ].; PDB: 3LUN_A 3LUM_B 2J83_A 2CKI_A.
Probab=48.56 E-value=9.1 Score=33.96 Aligned_cols=19 Identities=37% Similarity=0.721 Sum_probs=13.3
Q ss_pred ChhhhhhHHHHHhHHHHhhh
Q 016954 353 PRLLTGTILAHEMMHGWMRL 372 (380)
Q Consensus 353 p~~~~g~ilahe~~ha~l~l 372 (380)
+..-.|.+|+||++| ||=|
T Consensus 65 ~~~~~g~TltHEvGH-~LGL 83 (154)
T PF05572_consen 65 SQYNFGKTLTHEVGH-WLGL 83 (154)
T ss_dssp TTS-SSHHHHHHHHH-HTT-
T ss_pred Cccccccchhhhhhh-hhcc
Confidence 355668999999999 5544
No 68
>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=48.27 E-value=7.6 Score=38.71 Aligned_cols=14 Identities=36% Similarity=0.997 Sum_probs=12.1
Q ss_pred hhhHHHHHhHHHHh
Q 016954 357 TGTILAHEMMHGWM 370 (380)
Q Consensus 357 ~g~ilahe~~ha~l 370 (380)
...++|||++|.|.
T Consensus 295 ~~~~iahElahqWf 308 (390)
T PF01433_consen 295 IASLIAHELAHQWF 308 (390)
T ss_dssp HHHHHHHHHHTTTB
T ss_pred hHHHHHHHHHHHHh
Confidence 45789999999996
No 69
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=47.90 E-value=11 Score=22.69 Aligned_cols=8 Identities=50% Similarity=1.306 Sum_probs=4.0
Q ss_pred cccCCccc
Q 016954 116 CAGCNNEI 123 (380)
Q Consensus 116 C~~C~~~I 123 (380)
|..|+..|
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 44555554
No 70
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=47.16 E-value=12 Score=25.33 Aligned_cols=26 Identities=19% Similarity=0.273 Sum_probs=16.8
Q ss_pred cccCCccccc-CceEeeCCceecCCCc
Q 016954 116 CAGCNNEIGH-GRFLNCLDVFWHPECF 141 (380)
Q Consensus 116 C~~C~~~I~~-g~~v~alg~~wH~~CF 141 (380)
|.-|+.+|.. ..++...++.|+.-|-
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~ 27 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCP 27 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECH
Confidence 6778888842 2445677888874443
No 71
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=47.05 E-value=7.8 Score=35.34 Aligned_cols=48 Identities=19% Similarity=0.499 Sum_probs=37.0
Q ss_pred CCCcccCCCCCCCCCce-eeccCCccccccccccc--ccccccccCCcccC
Q 016954 138 PECFCCHACHQPITDIE-FSTSENRPYHKSCYREH--YHPKCDVCKHFIPS 185 (380)
Q Consensus 138 ~~CF~C~~C~~~L~~~~-f~~~dg~~YC~~cy~~~--f~pkC~~C~~~I~~ 185 (380)
..||.|..|-.+..... +.-.=|.+||+.|-+.. ...+|..|++.|..
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence 45788888877776654 66677899999998764 45689999998864
No 72
>PF14247 DUF4344: Domain of unknown function (DUF4344)
Probab=46.46 E-value=14 Score=34.83 Aligned_cols=21 Identities=24% Similarity=0.082 Sum_probs=18.0
Q ss_pred hhHHHHHhHHHHhhhcCCCCC
Q 016954 358 GTILAHEMMHGWMRLQGAFCL 378 (380)
Q Consensus 358 g~ilahe~~ha~l~l~g~~~l 378 (380)
-.||-||++||.+-+.+.|-|
T Consensus 93 ~~~l~HE~GHAlI~~~~lPv~ 113 (220)
T PF14247_consen 93 LFTLYHELGHALIDDLDLPVL 113 (220)
T ss_pred HHHHHHHHHHHHHHHhcCCcc
Confidence 367999999999999887765
No 73
>cd06161 S2P-M50_SpoIVFB 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. SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) 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.
Probab=45.78 E-value=14 Score=34.34 Aligned_cols=21 Identities=33% Similarity=0.471 Sum_probs=16.8
Q ss_pred hhhhhHHHHHhHHHHhhhc-CC
Q 016954 355 LLTGTILAHEMMHGWMRLQ-GA 375 (380)
Q Consensus 355 ~~~g~ilahe~~ha~l~l~-g~ 375 (380)
.++.+|+.||++|++.-.. |.
T Consensus 36 ~l~~~v~iHElgH~~~A~~~G~ 57 (208)
T cd06161 36 LLFLSVLLHELGHALVARRYGI 57 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHcCC
Confidence 5788999999999987543 54
No 74
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=45.73 E-value=12 Score=27.54 Aligned_cols=29 Identities=17% Similarity=0.555 Sum_probs=17.6
Q ss_pred CCccccCCccccc-CceEee--CCceecCCCc
Q 016954 113 YRICAGCNNEIGH-GRFLNC--LDVFWHPECF 141 (380)
Q Consensus 113 ~~~C~~C~~~I~~-g~~v~a--lg~~wH~~CF 141 (380)
..+|..|++.|.. +.+|.. =+..||.+|.
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 4689999999953 344432 2455555554
No 75
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=45.56 E-value=13 Score=25.67 Aligned_cols=21 Identities=29% Similarity=0.771 Sum_probs=14.8
Q ss_pred ccccCCcCCCCCceEEccCCcccChhh
Q 016954 215 CCSCERMEPQDTAYVALDDGRKLCLEC 241 (380)
Q Consensus 215 C~~C~r~l~~g~~f~~l~dg~~~C~~C 241 (380)
|..|+.++ +...+|+.||..|
T Consensus 20 Cp~C~~PL------~~~k~g~~~Cv~C 40 (41)
T PF06677_consen 20 CPDCGTPL------MRDKDGKIYCVSC 40 (41)
T ss_pred cCCCCCee------EEecCCCEECCCC
Confidence 66677666 3346888899877
No 76
>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=45.52 E-value=12 Score=33.69 Aligned_cols=13 Identities=31% Similarity=0.294 Sum_probs=10.9
Q ss_pred hhhHHHHHhHHHH
Q 016954 357 TGTILAHEMMHGW 369 (380)
Q Consensus 357 ~g~ilahe~~ha~ 369 (380)
.-.++|||++|.|
T Consensus 111 ~~~~~aHElGH~l 123 (173)
T PF13574_consen 111 GIDTFAHELGHQL 123 (173)
T ss_dssp HHHHHHHHHHHHH
T ss_pred eeeeehhhhHhhc
Confidence 4567999999987
No 77
>PF08219 TOM13: Outer membrane protein TOM13; InterPro: IPR013262 The TOM13 family of proteins are mitochondrial outer membrane proteins that mediate the assembly of beta-barrel proteins [].; GO: 0005741 mitochondrial outer membrane
Probab=45.47 E-value=15 Score=28.76 Aligned_cols=16 Identities=31% Similarity=0.397 Sum_probs=13.7
Q ss_pred hhhhhhHHHHHhHHHH
Q 016954 354 RLLTGTILAHEMMHGW 369 (380)
Q Consensus 354 ~~~~g~ilahe~~ha~ 369 (380)
.|=||.|+|||+.+-|
T Consensus 49 MLGFGEl~AhE~~fr~ 64 (77)
T PF08219_consen 49 MLGFGELFAHEIAFRL 64 (77)
T ss_pred hHhHHHHHHHHHHHHh
Confidence 5789999999998765
No 78
>COG1451 Predicted metal-dependent hydrolase [General function prediction only]
Probab=44.91 E-value=12 Score=35.42 Aligned_cols=27 Identities=19% Similarity=0.230 Sum_probs=21.8
Q ss_pred eEEEEEEecCCChhhhhhHHHHHhHHH
Q 016954 342 DVTAILILYGLPRLLTGTILAHEMMHG 368 (380)
Q Consensus 342 ~v~~il~l~glp~~~~g~ilahe~~ha 368 (380)
+++==+.|-.+|.-+..+|++||+.|-
T Consensus 160 ~i~~~~~l~~~p~~~i~YVvvHELaHL 186 (223)
T COG1451 160 EIRFNWRLVMAPEEVIDYVVVHELAHL 186 (223)
T ss_pred cEEeehhhhcCCHHHHHHHHHHHHHHH
Confidence 334445677899999999999999994
No 79
>cd06159 S2P-M50_PDZ_Arch Uncharacterized Archaeal 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 appears to be limited to Archaeal S2P/M50s homologs with additional putative N-terminal transmembrane spanning regions, relative to the core protein, and either one or two PDZ domains present.
Probab=44.65 E-value=14 Score=35.75 Aligned_cols=24 Identities=29% Similarity=0.560 Sum_probs=17.0
Q ss_pred EecCCChhhhhhHHHHHhHHHHhhh
Q 016954 348 ILYGLPRLLTGTILAHEMMHGWMRL 372 (380)
Q Consensus 348 ~l~glp~~~~g~ilahe~~ha~l~l 372 (380)
++|++. .+.-+++.||++||+.-.
T Consensus 110 ~~~~~i-aL~isv~iHElgHa~~Ar 133 (263)
T cd06159 110 LPYGII-ALVVGVVVHELSHGILAR 133 (263)
T ss_pred HHHHHH-HHHHHHHHHHHHHHHHHH
Confidence 334443 356689999999999754
No 80
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=44.48 E-value=12 Score=34.39 Aligned_cols=52 Identities=15% Similarity=0.284 Sum_probs=41.8
Q ss_pred CccCCCCcccccCCcCCCCCceEEccCCcccChhhhhhhccCCCCCCcchHHH
Q 016954 207 HEHDGTPRCCSCERMEPQDTAYVALDDGRKLCLECLDSAIMDTNECQPLYLDI 259 (380)
Q Consensus 207 h~H~~CF~C~~C~r~l~~g~~f~~l~dg~~~C~~C~~~~v~~~~~C~~c~~~I 259 (380)
.||..|..|..|...+..+...+.. +|..||...+.........|..|...|
T Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~ 69 (235)
T KOG0490|consen 18 YWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTI 69 (235)
T ss_pred HHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCc
Confidence 5799999999999887544555555 999999999987445677899998776
No 81
>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=44.21 E-value=15 Score=36.00 Aligned_cols=17 Identities=35% Similarity=0.354 Sum_probs=14.4
Q ss_pred hhhhHHHHHhHHHHhhh
Q 016954 356 LTGTILAHEMMHGWMRL 372 (380)
Q Consensus 356 ~~g~ilahe~~ha~l~l 372 (380)
+.-+++.||++||+.-.
T Consensus 134 l~isvvvHElgHal~A~ 150 (277)
T cd06162 134 LLISGVVHEMGHGVAAV 150 (277)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 46788999999999865
No 82
>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=43.99 E-value=22 Score=32.06 Aligned_cols=16 Identities=38% Similarity=0.486 Sum_probs=13.5
Q ss_pred hhhhhhHHHHHhHHHH
Q 016954 354 RLLTGTILAHEMMHGW 369 (380)
Q Consensus 354 ~~~~g~ilahe~~ha~ 369 (380)
.+.+..|+|||++|.+
T Consensus 128 ~~~~a~~~AHElGH~l 143 (194)
T cd04269 128 LLLFAVTMAHELGHNL 143 (194)
T ss_pred hHHHHHHHHHHHHhhc
Confidence 4677899999999975
No 83
>KOG3714 consensus Meprin A metalloprotease [Posttranslational modification, protein turnover, chaperones]
Probab=43.76 E-value=11 Score=38.95 Aligned_cols=23 Identities=30% Similarity=0.534 Sum_probs=15.8
Q ss_pred cccccccceeEEEEEEecCCChhhhhhHHHHHhHHHH
Q 016954 333 EPYKLTRRCDVTAILILYGLPRLLTGTILAHEMMHGW 369 (380)
Q Consensus 333 ~~~~~~~~~~v~~il~l~glp~~~~g~ilahe~~ha~ 369 (380)
|+..+...|.-. .|.+||+|||=
T Consensus 149 q~~sl~~~C~~~--------------G~i~HEl~HaL 171 (411)
T KOG3714|consen 149 QLLSLGDGCDRF--------------GTIVHELMHAL 171 (411)
T ss_pred cceecCCCcCcC--------------chhHHHHHHHh
Confidence 444567777642 46799999983
No 84
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=43.63 E-value=15 Score=25.84 Aligned_cols=42 Identities=19% Similarity=0.490 Sum_probs=27.6
Q ss_pred ccCCCCCCCCCceeeccCCcc-ccccccccc--ccccccccCCccc
Q 016954 142 CCHACHQPITDIEFSTSENRP-YHKSCYREH--YHPKCDVCKHFIP 184 (380)
Q Consensus 142 ~C~~C~~~L~~~~f~~~dg~~-YC~~cy~~~--f~pkC~~C~~~I~ 184 (380)
.|..|........+. .=|.. +|..|+.+. ...+|..|.++|.
T Consensus 4 ~C~iC~~~~~~~~~~-pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 4 ECPICFENPRDVVLL-PCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp B-TTTSSSBSSEEEE-TTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred CCccCCccCCceEEe-CCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 466666665553333 34555 899998776 4679999999886
No 85
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=43.18 E-value=18 Score=25.31 Aligned_cols=43 Identities=23% Similarity=0.422 Sum_probs=31.2
Q ss_pred cccccCCcCCCCCceEEccCCcc-cChhhhhhhccCCCCCCcchHHH
Q 016954 214 RCCSCERMEPQDTAYVALDDGRK-LCLECLDSAIMDTNECQPLYLDI 259 (380)
Q Consensus 214 ~C~~C~r~l~~g~~f~~l~dg~~-~C~~C~~~~v~~~~~C~~c~~~I 259 (380)
.|..|.... ...+.+.=|+. +|..|..++......|.-|+.+|
T Consensus 4 ~C~iC~~~~---~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i 47 (50)
T PF13920_consen 4 ECPICFENP---RDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPI 47 (50)
T ss_dssp B-TTTSSSB---SSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-
T ss_pred CCccCCccC---CceEEeCCCChHHHHHHhHHhcccCCCCCcCChhh
Confidence 577777543 22445678888 99999999887888999998766
No 86
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=43.00 E-value=12 Score=32.38 Aligned_cols=25 Identities=24% Similarity=0.505 Sum_probs=19.9
Q ss_pred cccccCCcCCCCCceEEccCCcccChhhhhhh
Q 016954 214 RCCSCERMEPQDTAYVALDDGRKLCLECLDSA 245 (380)
Q Consensus 214 ~C~~C~r~l~~g~~f~~l~dg~~~C~~C~~~~ 245 (380)
.|..|+.+| |. +||.+||..|-.+.
T Consensus 30 hCp~Cg~PL------F~-KdG~v~CPvC~~~~ 54 (131)
T COG1645 30 HCPKCGTPL------FR-KDGEVFCPVCGYRE 54 (131)
T ss_pred hCcccCCcc------ee-eCCeEECCCCCceE
Confidence 388999887 43 79999999998543
No 87
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=42.82 E-value=15 Score=29.92 Aligned_cols=24 Identities=21% Similarity=0.515 Sum_probs=17.7
Q ss_pred CcccccccccccccccccccCCcccC
Q 016954 160 NRPYHKSCYREHYHPKCDVCKHFIPS 185 (380)
Q Consensus 160 g~~YC~~cy~~~f~pkC~~C~~~I~~ 185 (380)
|.-||..|..+ .-.|.-|++.|.+
T Consensus 58 g~~YCq~CAYk--kGiCamCGKki~d 81 (90)
T PF10235_consen 58 GAKYCQTCAYK--KGICAMCGKKILD 81 (90)
T ss_pred CCccChhhhcc--cCcccccCCeecc
Confidence 56788888655 3488888888865
No 88
>PRK14015 pepN aminopeptidase N; Provisional
Probab=42.77 E-value=12 Score=42.36 Aligned_cols=14 Identities=36% Similarity=0.937 Sum_probs=12.0
Q ss_pred hhhHHHHHhHHHHh
Q 016954 357 TGTILAHEMMHGWM 370 (380)
Q Consensus 357 ~g~ilahe~~ha~l 370 (380)
..+|+|||+.|.|.
T Consensus 296 i~~vIaHElaHqWF 309 (875)
T PRK14015 296 IESVIAHEYFHNWT 309 (875)
T ss_pred HHHHHHHHHHHHHH
Confidence 45799999999994
No 89
>PRK04897 heat shock protein HtpX; Provisional
Probab=42.76 E-value=11 Score=36.95 Aligned_cols=18 Identities=22% Similarity=0.222 Sum_probs=14.7
Q ss_pred CCChhhhhhHHHHHhHHH
Q 016954 351 GLPRLLTGTILAHEMMHG 368 (380)
Q Consensus 351 glp~~~~g~ilahe~~ha 368 (380)
.|++.-..+|||||++|.
T Consensus 131 ~l~~~El~aVlAHElgHi 148 (298)
T PRK04897 131 IMNREELEGVIGHEISHI 148 (298)
T ss_pred hCCHHHHHHHHHHHHHHH
Confidence 456667789999999995
No 90
>PRK05580 primosome assembly protein PriA; Validated
Probab=42.28 E-value=20 Score=39.43 Aligned_cols=38 Identities=16% Similarity=0.385 Sum_probs=25.9
Q ss_pred ccCCCCCCCCCceeeccCCccccccccccc-ccccccccCCc
Q 016954 142 CCHACHQPITDIEFSTSENRPYHKSCYREH-YHPKCDVCKHF 182 (380)
Q Consensus 142 ~C~~C~~~L~~~~f~~~dg~~YC~~cy~~~-f~pkC~~C~~~ 182 (380)
+|..|+.+| .|....+.+.|..|-... ...+|..|+..
T Consensus 392 ~C~~C~~~l---~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 392 ECPHCDASL---TLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred CCCCCCCce---eEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 567777666 344456778888886543 45689999775
No 91
>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=42.24 E-value=16 Score=34.39 Aligned_cols=21 Identities=33% Similarity=0.547 Sum_probs=16.4
Q ss_pred hhhhhHHHHHhHHHHhhhc-CC
Q 016954 355 LLTGTILAHEMMHGWMRLQ-GA 375 (380)
Q Consensus 355 ~~~g~ilahe~~ha~l~l~-g~ 375 (380)
+++.+|+.||++|++.-.. |+
T Consensus 51 ~l~~~v~iHElgH~~~A~~~G~ 72 (227)
T cd06164 51 LLFASVLLHELGHSLVARRYGI 72 (227)
T ss_pred HHHHHHHHHHHHHHHHHHHcCC
Confidence 5788999999999986433 44
No 92
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=41.91 E-value=12 Score=34.75 Aligned_cols=15 Identities=20% Similarity=0.494 Sum_probs=11.2
Q ss_pred ccCCccccccccccc
Q 016954 157 TSENRPYHKSCYREH 171 (380)
Q Consensus 157 ~~dg~~YC~~cy~~~ 171 (380)
..+|++.|..||.+.
T Consensus 189 ~~ng~~vC~~C~~~~ 203 (206)
T COG2191 189 VLNGKPVCKPCAEKK 203 (206)
T ss_pred hcCCceecccccccc
Confidence 457888888888753
No 93
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=41.87 E-value=4.3 Score=33.27 Aligned_cols=49 Identities=22% Similarity=0.513 Sum_probs=29.1
Q ss_pred cccCCcccccCceEeeCCceecCCCcccCCCCCCCCCceeeccCCcccc
Q 016954 116 CAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYH 164 (380)
Q Consensus 116 C~~C~~~I~~g~~v~alg~~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC 164 (380)
|..|...+..-.+....-..+++.+..|..|...|+-.+|.+...=|||
T Consensus 38 Cy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C 86 (105)
T COG4357 38 CYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYC 86 (105)
T ss_pred HHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCc
Confidence 5566666543344444446677777777777777766666554443333
No 94
>PRK01345 heat shock protein HtpX; Provisional
Probab=41.30 E-value=22 Score=35.27 Aligned_cols=18 Identities=28% Similarity=0.307 Sum_probs=13.5
Q ss_pred CChhhhhhHHHHHhHHHH
Q 016954 352 LPRLLTGTILAHEMMHGW 369 (380)
Q Consensus 352 lp~~~~g~ilahe~~ha~ 369 (380)
|...=.-+|||||++|.-
T Consensus 119 L~~dEL~aVlAHElgHi~ 136 (317)
T PRK01345 119 LSPEEVAGVMAHELAHVK 136 (317)
T ss_pred CCHHHHHHHHHHHHHHHH
Confidence 344555789999999964
No 95
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=41.01 E-value=7.7 Score=36.18 Aligned_cols=37 Identities=16% Similarity=0.156 Sum_probs=27.4
Q ss_pred CccCCCCcccccCCcCCCCCceEEccCCcccChhhhhhh
Q 016954 207 HEHDGTPRCCSCERMEPQDTAYVALDDGRKLCLECLDSA 245 (380)
Q Consensus 207 h~H~~CF~C~~C~r~l~~g~~f~~l~dg~~~C~~C~~~~ 245 (380)
.||..||+|..|+..+. =.+|- -.|.++||-.+|..-
T Consensus 26 ~whk~cfkce~c~mtln-mKnyK-gy~kkpycn~hYpkq 62 (264)
T KOG1702|consen 26 VWHKQCFKCEVCGMTLN-MKNYK-GYDKKPYCNPHYPKQ 62 (264)
T ss_pred HHHHHhheeeeccCChh-hhhcc-ccccCCCcCcccccc
Confidence 37999999999997663 22332 248899999999753
No 96
>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=40.96 E-value=14 Score=32.19 Aligned_cols=14 Identities=29% Similarity=0.228 Sum_probs=11.8
Q ss_pred hhhhhHHHHHhHHH
Q 016954 355 LLTGTILAHEMMHG 368 (380)
Q Consensus 355 ~~~g~ilahe~~ha 368 (380)
.-.-+|+.||++||
T Consensus 102 ~~~~~~~~HEiGHa 115 (156)
T cd04279 102 ENLQAIALHELGHA 115 (156)
T ss_pred hHHHHHHHHHhhhh
Confidence 45568999999998
No 97
>PRK00420 hypothetical protein; Validated
Probab=40.90 E-value=16 Score=30.92 Aligned_cols=26 Identities=23% Similarity=0.342 Sum_probs=19.6
Q ss_pred cccccCCcCCCCCceEEccCCcccChhhhhhh
Q 016954 214 RCCSCERMEPQDTAYVALDDGRKLCLECLDSA 245 (380)
Q Consensus 214 ~C~~C~r~l~~g~~f~~l~dg~~~C~~C~~~~ 245 (380)
.|..|+.++ +.+.+|..+|..|-...
T Consensus 25 ~CP~Cg~pL------f~lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 25 HCPVCGLPL------FELKDGEVVCPVHGKVY 50 (112)
T ss_pred CCCCCCCcc------eecCCCceECCCCCCee
Confidence 477788665 44579999999997754
No 98
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=40.27 E-value=15 Score=25.03 Aligned_cols=42 Identities=19% Similarity=0.330 Sum_probs=27.7
Q ss_pred cccccCCcCCCCCceEEccCCcccChhhhhhhccCCCCCCcc
Q 016954 214 RCCSCERMEPQDTAYVALDDGRKLCLECLDSAIMDTNECQPL 255 (380)
Q Consensus 214 ~C~~C~r~l~~g~~f~~l~dg~~~C~~C~~~~v~~~~~C~~c 255 (380)
.|..|-..+..++..+.+.=|..+|..|..+.+.....|.-|
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~C 43 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVC 43 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTT
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCcc
Confidence 367777666556666777778888888887765544444443
No 99
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=39.65 E-value=16 Score=31.80 Aligned_cols=21 Identities=24% Similarity=0.774 Sum_probs=13.6
Q ss_pred cCCCCCCCCCceeeccCCcccccccc
Q 016954 143 CHACHQPITDIEFSTSENRPYHKSCY 168 (380)
Q Consensus 143 C~~C~~~L~~~~f~~~dg~~YC~~cy 168 (380)
|..|+.|| | ..+|.+||..|-
T Consensus 31 Cp~Cg~PL----F-~KdG~v~CPvC~ 51 (131)
T COG1645 31 CPKCGTPL----F-RKDGEVFCPVCG 51 (131)
T ss_pred CcccCCcc----e-eeCCeEECCCCC
Confidence 55566655 2 378888887764
No 100
>KOG3931 consensus Uncharacterized conserved protein [Function unknown]
Probab=38.65 E-value=18 Score=36.41 Aligned_cols=22 Identities=32% Similarity=0.493 Sum_probs=17.0
Q ss_pred ChhhhhhHHHHHhHHHHhhhcC
Q 016954 353 PRLLTGTILAHEMMHGWMRLQG 374 (380)
Q Consensus 353 p~~~~g~ilahe~~ha~l~l~g 374 (380)
||-=.=..|-|||.||||++..
T Consensus 101 PRkDLVETLLHEMIHAYlFV~n 122 (484)
T KOG3931|consen 101 PRKDLVETLLHEMIHAYLFVTN 122 (484)
T ss_pred chHHHHHHHHHHHHHHheeEec
Confidence 6654556788999999998753
No 101
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=38.56 E-value=7.6 Score=32.37 Aligned_cols=20 Identities=40% Similarity=0.745 Sum_probs=14.1
Q ss_pred CCCCccccCCcccccCceEee
Q 016954 111 EGYRICAGCNNEIGHGRFLNC 131 (380)
Q Consensus 111 ~~~~~C~~C~~~I~~g~~v~a 131 (380)
.+.+.|..|+++|. -..+.+
T Consensus 78 g~yG~C~~Cge~I~-~~RL~a 97 (110)
T TIGR02420 78 GEYGYCEECGEEIG-LRRLEA 97 (110)
T ss_pred CCCCchhccCCccc-HHHHhh
Confidence 45679999999994 333433
No 102
>PF06037 DUF922: Bacterial protein of unknown function (DUF922); InterPro: IPR010321 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=38.40 E-value=50 Score=29.54 Aligned_cols=29 Identities=31% Similarity=0.551 Sum_probs=21.2
Q ss_pred EEEEecCCChh----------------hhhhHHHHHhHHHHhhhc
Q 016954 345 AILILYGLPRL----------------LTGTILAHEMMHGWMRLQ 373 (380)
Q Consensus 345 ~il~l~glp~~----------------~~g~ilahe~~ha~l~l~ 373 (380)
-+-|-|=||++ +...|-+||.+|+=+-.+
T Consensus 58 ~l~itytlPr~~~~~~~~~~~~~~W~~~~a~l~~HE~~H~~ia~~ 102 (161)
T PF06037_consen 58 KLDITYTLPRWSRRAKAPPELRQRWDRFSAGLRRHEEVHGRIARE 102 (161)
T ss_pred EEEEEEECCCccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44566778887 366789999999866543
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=38.21 E-value=15 Score=39.69 Aligned_cols=12 Identities=42% Similarity=1.088 Sum_probs=11.2
Q ss_pred hHHHHHhHHHHh
Q 016954 359 TILAHEMMHGWM 370 (380)
Q Consensus 359 ~ilahe~~ha~l 370 (380)
.|+|||++|.|.
T Consensus 281 ~viaHElAHqWf 292 (601)
T TIGR02411 281 DVIAHELAHSWS 292 (601)
T ss_pred hhHHHHHHhhcc
Confidence 699999999996
No 104
>PRK05457 heat shock protein HtpX; Provisional
Probab=38.05 E-value=16 Score=35.60 Aligned_cols=19 Identities=32% Similarity=0.375 Sum_probs=15.9
Q ss_pred cCCChhhhhhHHHHHhHHH
Q 016954 350 YGLPRLLTGTILAHEMMHG 368 (380)
Q Consensus 350 ~glp~~~~g~ilahe~~ha 368 (380)
.-|++.---+|+|||++|.
T Consensus 127 ~~L~~~El~aVlAHElgHi 145 (284)
T PRK05457 127 QNMSRDEVEAVLAHEISHI 145 (284)
T ss_pred hhCCHHHHHHHHHHHHHHH
Confidence 3477777889999999996
No 105
>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=37.68 E-value=16 Score=33.85 Aligned_cols=10 Identities=40% Similarity=0.524 Sum_probs=8.8
Q ss_pred HHHHHhHHHH
Q 016954 360 ILAHEMMHGW 369 (380)
Q Consensus 360 ilahe~~ha~ 369 (380)
+++||+|||-
T Consensus 90 ti~HEl~HaL 99 (200)
T cd04281 90 IVVHELGHVI 99 (200)
T ss_pred hHHHHHHHHh
Confidence 7899999983
No 106
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=37.53 E-value=11 Score=28.17 Aligned_cols=10 Identities=40% Similarity=0.916 Sum_probs=5.0
Q ss_pred ccccccCCcc
Q 016954 174 PKCDVCKHFI 183 (380)
Q Consensus 174 pkC~~C~~~I 183 (380)
+.|..|+..|
T Consensus 10 ~~CtSCg~~i 19 (61)
T COG2888 10 PVCTSCGREI 19 (61)
T ss_pred ceeccCCCEe
Confidence 4455555544
No 107
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=36.83 E-value=19 Score=36.38 Aligned_cols=46 Identities=30% Similarity=0.359 Sum_probs=30.2
Q ss_pred cccccceeeccccCCCCCccccccccccccccceeEEEEEEecCCChhhh-----hhHHHHHhHHH
Q 016954 308 EEQTVTTVLWRPRFGPGNQARNIITEPYKLTRRCDVTAILILYGLPRLLT-----GTILAHEMMHG 368 (380)
Q Consensus 308 E~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~il~l~glp~~~~-----g~ilahe~~ha 368 (380)
..+|+-||+..|.|. -+ .|.. --|+|-.||=.|+- .+||||||+|+
T Consensus 85 ~q~YriTilnSP~IN---AF--------ALPG----GYlYitRGLlAland~sEvAAVl~HEmgHV 135 (479)
T COG4784 85 QQTYRITILNSPNIN---AF--------ALPG----GYLYITRGLLALANDSSEVAAVLAHEMGHV 135 (479)
T ss_pred CceEEEEEecCCCcc---cc--------ccCC----ceEEEehhHHHHcCCHHHHHHHHHhhhhhe
Confidence 456788899888772 11 1111 12567777776663 57899999996
No 108
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=36.82 E-value=30 Score=38.34 Aligned_cols=39 Identities=15% Similarity=0.385 Sum_probs=27.7
Q ss_pred cccCCCCCCCCCceeeccCCcccccccccc-cccccccccCCc
Q 016954 141 FCCHACHQPITDIEFSTSENRPYHKSCYRE-HYHPKCDVCKHF 182 (380)
Q Consensus 141 F~C~~C~~~L~~~~f~~~dg~~YC~~cy~~-~f~pkC~~C~~~ 182 (380)
++|..|+.+| .|....+.+.|..|-.+ ..-..|..|+..
T Consensus 445 ~~Cp~Cd~~l---t~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPL---TLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcce---EEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 4788888877 34455678888888665 334478888876
No 109
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 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 PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=36.39 E-value=15 Score=28.59 Aligned_cols=17 Identities=35% Similarity=0.909 Sum_probs=12.6
Q ss_pred CCCCccccCCcccccCc
Q 016954 111 EGYRICAGCNNEIGHGR 127 (380)
Q Consensus 111 ~~~~~C~~C~~~I~~g~ 127 (380)
.+-..|.+|++.|..|.
T Consensus 5 s~Ra~Ck~C~~~I~kg~ 21 (82)
T PF00645_consen 5 SGRAKCKGCKKKIAKGE 21 (82)
T ss_dssp SSTEBETTTSCBE-TTS
T ss_pred CCCccCcccCCcCCCCC
Confidence 45678999999997664
No 110
>PRK03001 M48 family peptidase; Provisional
Probab=36.15 E-value=18 Score=35.17 Aligned_cols=18 Identities=28% Similarity=0.304 Sum_probs=13.6
Q ss_pred CChhhhhhHHHHHhHHHH
Q 016954 352 LPRLLTGTILAHEMMHGW 369 (380)
Q Consensus 352 lp~~~~g~ilahe~~ha~ 369 (380)
|...=.-+|||||++|.=
T Consensus 119 l~~~El~aVlAHElgHi~ 136 (283)
T PRK03001 119 LSEREIRGVMAHELAHVK 136 (283)
T ss_pred CCHHHHHHHHHHHHHHHh
Confidence 445556689999999963
No 111
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=35.99 E-value=27 Score=22.65 Aligned_cols=41 Identities=24% Similarity=0.436 Sum_probs=24.0
Q ss_pred ccccCCcCCCCCceEEccCCcccChhhhhhhccC-CCCCCcchH
Q 016954 215 CCSCERMEPQDTAYVALDDGRKLCLECLDSAIMD-TNECQPLYL 257 (380)
Q Consensus 215 C~~C~r~l~~g~~f~~l~dg~~~C~~C~~~~v~~-~~~C~~c~~ 257 (380)
|..|...+ ...+....=|..+|..|....... ...|..|..
T Consensus 2 C~iC~~~~--~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~ 43 (45)
T cd00162 2 CPICLEEF--REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRT 43 (45)
T ss_pred CCcCchhh--hCceEecCCCChhcHHHHHHHHHhCcCCCCCCCC
Confidence 55666444 233333446788888888765443 455666653
No 112
>PRK02870 heat shock protein HtpX; Provisional
Probab=35.80 E-value=20 Score=36.03 Aligned_cols=24 Identities=33% Similarity=0.403 Sum_probs=16.7
Q ss_pred EEEEecCC----ChhhhhhHHHHHhHHH
Q 016954 345 AILILYGL----PRLLTGTILAHEMMHG 368 (380)
Q Consensus 345 ~il~l~gl----p~~~~g~ilahe~~ha 368 (380)
.|.|-.|| .+.=..+|||||++|.
T Consensus 157 ~Ivvt~GLL~~L~~dEL~aVlAHELgHi 184 (336)
T PRK02870 157 MVAITTGLLEKLDRDELQAVMAHELSHI 184 (336)
T ss_pred EEEEehHHhhhCCHHHHHHHHHHHHHHH
Confidence 34554444 4555678999999997
No 113
>PRK03982 heat shock protein HtpX; Provisional
Probab=35.63 E-value=19 Score=35.10 Aligned_cols=18 Identities=28% Similarity=0.217 Sum_probs=13.9
Q ss_pred CChhhhhhHHHHHhHHHH
Q 016954 352 LPRLLTGTILAHEMMHGW 369 (380)
Q Consensus 352 lp~~~~g~ilahe~~ha~ 369 (380)
|...=--+|||||++|.=
T Consensus 120 l~~~El~AVlAHElgHi~ 137 (288)
T PRK03982 120 LNEDELEGVIAHELTHIK 137 (288)
T ss_pred CCHHHHHHHHHHHHHHHH
Confidence 455556789999999963
No 114
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=35.53 E-value=20 Score=34.38 Aligned_cols=19 Identities=32% Similarity=0.116 Sum_probs=14.2
Q ss_pred CCChhhhhhHHHHHhHHHH
Q 016954 351 GLPRLLTGTILAHEMMHGW 369 (380)
Q Consensus 351 glp~~~~g~ilahe~~ha~ 369 (380)
-|...---+|||||++|.-
T Consensus 151 ~l~~dEl~aVlaHElgHi~ 169 (302)
T COG0501 151 LLNDDELEAVLAHELGHIK 169 (302)
T ss_pred hCCHHHHHHHHHHHHHHHh
Confidence 3455555689999999974
No 115
>PRK03072 heat shock protein HtpX; Provisional
Probab=35.43 E-value=18 Score=35.31 Aligned_cols=19 Identities=26% Similarity=0.181 Sum_probs=14.2
Q ss_pred cCCChhhhhhHHHHHhHHH
Q 016954 350 YGLPRLLTGTILAHEMMHG 368 (380)
Q Consensus 350 ~glp~~~~g~ilahe~~ha 368 (380)
.-|.+.=.-+|||||++|.
T Consensus 120 ~~l~~~El~aVlAHElgHi 138 (288)
T PRK03072 120 QILNERELRGVLGHELSHV 138 (288)
T ss_pred HhCCHHHHHHHHHHHHHHH
Confidence 3455555678999999995
No 116
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.97 E-value=20 Score=35.17 Aligned_cols=46 Identities=22% Similarity=0.416 Sum_probs=32.3
Q ss_pred CcccCCCCCCCCCceeeccCCcccccccccccc--cccccccCCcccCC
Q 016954 140 CFCCHACHQPITDIEFSTSENRPYHKSCYREHY--HPKCDVCKHFIPSN 186 (380)
Q Consensus 140 CF~C~~C~~~L~~~~f~~~dg~~YC~~cy~~~f--~pkC~~C~~~I~~~ 186 (380)
=|.|..|++..... ....-+..+|+.|....| +++|.+|++.+.+.
T Consensus 241 Pf~c~icr~~f~~p-Vvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~ 288 (313)
T KOG1813|consen 241 PFKCFICRKYFYRP-VVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHGS 288 (313)
T ss_pred Cccccccccccccc-hhhcCCceeehhhhccccccCCcceecccccccc
Confidence 47788888776542 222345678999987654 47999999988763
No 117
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=34.66 E-value=15 Score=34.12 Aligned_cols=30 Identities=20% Similarity=0.619 Sum_probs=22.8
Q ss_pred CcccccCCcCCCCCceEEccCCcccChhhhhh
Q 016954 213 PRCCSCERMEPQDTAYVALDDGRKLCLECLDS 244 (380)
Q Consensus 213 F~C~~C~r~l~~g~~f~~l~dg~~~C~~C~~~ 244 (380)
-+|..|+.++.... ..+.+|+++|..|+..
T Consensus 173 v~C~kCGE~~~e~~--~~~~ng~~vC~~C~~~ 202 (206)
T COG2191 173 VRCSKCGELFMEPR--AVVLNGKPVCKPCAEK 202 (206)
T ss_pred eeccccCcccccch--hhhcCCceeccccccc
Confidence 47999997764332 3456999999999975
No 118
>PF13582 Reprolysin_3: Metallo-peptidase family M12B Reprolysin-like; PDB: 3P24_C.
Probab=34.62 E-value=21 Score=29.54 Aligned_cols=11 Identities=36% Similarity=0.549 Sum_probs=9.9
Q ss_pred hHHHHHhHHHH
Q 016954 359 TILAHEMMHGW 369 (380)
Q Consensus 359 ~ilahe~~ha~ 369 (380)
.++|||++|.+
T Consensus 109 ~~~~HEiGH~l 119 (124)
T PF13582_consen 109 DTFAHEIGHNL 119 (124)
T ss_dssp THHHHHHHHHT
T ss_pred eEeeehhhHhc
Confidence 89999999974
No 119
>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=34.52 E-value=21 Score=36.31 Aligned_cols=13 Identities=38% Similarity=0.378 Sum_probs=10.8
Q ss_pred hhhhHHHHHhHHH
Q 016954 356 LTGTILAHEMMHG 368 (380)
Q Consensus 356 ~~g~ilahe~~ha 368 (380)
.+=++||||++|+
T Consensus 138 ~~~sTlAHEfQHm 150 (366)
T PF10460_consen 138 TVYSTLAHEFQHM 150 (366)
T ss_pred HHHHHHHHHHHHH
Confidence 3558899999997
No 120
>PF09471 Peptidase_M64: IgA Peptidase M64; InterPro: IPR019026 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 is a family of highly selective metallo-endopeptidases belonging to the MEROPS peptidase family M64 (IgA peptidase, clan MA). The primary structure of the Clostridium ramosum IgA peptidase shows no significant overall similarity to any other known metallo-endopeptidase []. ; PDB: 3P1V_A 4DF9_D.
Probab=34.46 E-value=23 Score=34.40 Aligned_cols=19 Identities=21% Similarity=0.295 Sum_probs=14.3
Q ss_pred hhhhHHHHHhHHHHhhhcC
Q 016954 356 LTGTILAHEMMHGWMRLQG 374 (380)
Q Consensus 356 ~~g~ilahe~~ha~l~l~g 374 (380)
.+..|+.||++|.+..|..
T Consensus 215 ~~~~v~vHE~GHsf~~LaD 233 (264)
T PF09471_consen 215 SFKQVVVHEFGHSFGGLAD 233 (264)
T ss_dssp THHHHHHHHHHHHTT----
T ss_pred cccceeeeecccccccccc
Confidence 7899999999999999975
No 121
>TIGR00181 pepF oligoendopeptidase F. This family represents the oligoendopeptidase F clade of the family of larger M3 or thimet (for thiol-dependent metallopeptidase) oligopeptidase family. Lactococcus lactis PepF hydrolyzed peptides of 7 and 17 amino acids with fairly broad specificity. The homolog of lactococcal PepF in group B Streptococcus was named PepB (PubMed:8757883), with the name difference reflecting a difference in species of origin rather activity; substrate profiles were quite similar. Differences in substrate specificity should be expected in other species. The gene is duplicated in Lactococcus lactis on the plasmid that bears it. A shortened second copy is found in Bacillus subtilis.
Probab=34.22 E-value=20 Score=38.48 Aligned_cols=11 Identities=45% Similarity=0.543 Sum_probs=9.9
Q ss_pred hHHHHHhHHHH
Q 016954 359 TILAHEMMHGW 369 (380)
Q Consensus 359 ~ilahe~~ha~ 369 (380)
.+||||++||+
T Consensus 380 ~TLaHElGHa~ 390 (591)
T TIGR00181 380 FTLAHELGHSM 390 (591)
T ss_pred HHHHHHhhhHH
Confidence 56999999997
No 122
>PF13583 Reprolysin_4: Metallo-peptidase family M12B Reprolysin-like
Probab=34.09 E-value=21 Score=33.11 Aligned_cols=11 Identities=36% Similarity=0.549 Sum_probs=9.8
Q ss_pred hHHHHHhHHHH
Q 016954 359 TILAHEMMHGW 369 (380)
Q Consensus 359 ~ilahe~~ha~ 369 (380)
.++|||++|++
T Consensus 139 ~~~aHEiGH~l 149 (206)
T PF13583_consen 139 QTFAHEIGHNL 149 (206)
T ss_pred hHHHHHHHHHh
Confidence 67999999986
No 123
>PRK02391 heat shock protein HtpX; Provisional
Probab=33.98 E-value=19 Score=35.45 Aligned_cols=19 Identities=32% Similarity=0.227 Sum_probs=14.4
Q ss_pred CCChhhhhhHHHHHhHHHH
Q 016954 351 GLPRLLTGTILAHEMMHGW 369 (380)
Q Consensus 351 glp~~~~g~ilahe~~ha~ 369 (380)
.|...=.-+|||||++|.-
T Consensus 127 ~L~~~El~aVlaHElgHi~ 145 (296)
T PRK02391 127 RLDPDELEAVLAHELSHVK 145 (296)
T ss_pred hCCHHHHHHHHHHHHHHHH
Confidence 4555556789999999964
No 124
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=33.88 E-value=39 Score=22.34 Aligned_cols=37 Identities=22% Similarity=0.523 Sum_probs=23.6
Q ss_pred ccccCCcCCCCCceEEccCCcccChhhhhhhccCCCCCC
Q 016954 215 CCSCERMEPQDTAYVALDDGRKLCLECLDSAIMDTNECQ 253 (380)
Q Consensus 215 C~~C~r~l~~g~~f~~l~dg~~~C~~C~~~~v~~~~~C~ 253 (380)
|..|...+ .+..+.+.=|+.||.+|..+.+.....|.
T Consensus 1 C~iC~~~~--~~~~~~~~CGH~fC~~C~~~~~~~~~~CP 37 (39)
T PF13923_consen 1 CPICLDEL--RDPVVVTPCGHSFCKECIEKYLEKNPKCP 37 (39)
T ss_dssp ETTTTSB---SSEEEECTTSEEEEHHHHHHHHHCTSB-T
T ss_pred CCCCCCcc--cCcCEECCCCCchhHHHHHHHHHCcCCCc
Confidence 45565543 23545678899999999987665544443
No 125
>cd04272 ZnMc_salivary_gland_MPs Zinc-dependent metalloprotease, salivary_gland_MPs. Metalloproteases secreted by the salivary glands of arthropods.
Probab=33.62 E-value=26 Score=32.48 Aligned_cols=15 Identities=20% Similarity=0.204 Sum_probs=12.2
Q ss_pred hhhhhHHHHHhHHHH
Q 016954 355 LLTGTILAHEMMHGW 369 (380)
Q Consensus 355 ~~~g~ilahe~~ha~ 369 (380)
+....++|||++|..
T Consensus 143 ~~~~~~~AHElGH~l 157 (220)
T cd04272 143 YYGVYTMTHELAHLL 157 (220)
T ss_pred cccHHHHHHHHHHHh
Confidence 455789999999964
No 126
>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=33.56 E-value=20 Score=34.01 Aligned_cols=11 Identities=27% Similarity=0.655 Sum_probs=9.2
Q ss_pred hHHHHHhHHHH
Q 016954 359 TILAHEMMHGW 369 (380)
Q Consensus 359 ~ilahe~~ha~ 369 (380)
.+++||+|||-
T Consensus 122 Gti~HEl~Hal 132 (230)
T cd04282 122 ATVEHEFLHAL 132 (230)
T ss_pred chHHHHHHHHh
Confidence 47899999983
No 127
>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=33.19 E-value=21 Score=40.34 Aligned_cols=14 Identities=36% Similarity=0.937 Sum_probs=12.0
Q ss_pred hhhHHHHHhHHHHh
Q 016954 357 TGTILAHEMMHGWM 370 (380)
Q Consensus 357 ~g~ilahe~~ha~l 370 (380)
..+|+|||+.|.|.
T Consensus 283 i~~VIaHElaHqWf 296 (863)
T TIGR02414 283 IESVIAHEYFHNWT 296 (863)
T ss_pred HHHHHHHHHHHHHh
Confidence 34799999999994
No 128
>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=32.75 E-value=19 Score=31.48 Aligned_cols=15 Identities=27% Similarity=0.182 Sum_probs=12.0
Q ss_pred hhhhhhHHHHHhHHH
Q 016954 354 RLLTGTILAHEMMHG 368 (380)
Q Consensus 354 ~~~~g~ilahe~~ha 368 (380)
..-+-.|+.||++||
T Consensus 104 ~~~~~~~~~HEiGHa 118 (157)
T cd04278 104 GTDLFSVAAHEIGHA 118 (157)
T ss_pred cchHHHHHHHHhccc
Confidence 344568999999998
No 129
>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=32.63 E-value=27 Score=31.89 Aligned_cols=13 Identities=23% Similarity=0.391 Sum_probs=10.3
Q ss_pred hhhHHHHHhHHHH
Q 016954 357 TGTILAHEMMHGW 369 (380)
Q Consensus 357 ~g~ilahe~~ha~ 369 (380)
+..++.||+|||-
T Consensus 92 ~~~~i~HElgHaL 104 (198)
T cd04327 92 FSRVVLHEFGHAL 104 (198)
T ss_pred HHHHHHHHHHHHh
Confidence 3458889999984
No 130
>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=32.55 E-value=23 Score=32.42 Aligned_cols=10 Identities=40% Similarity=0.906 Sum_probs=8.8
Q ss_pred hHHHHHhHHH
Q 016954 359 TILAHEMMHG 368 (380)
Q Consensus 359 ~ilahe~~ha 368 (380)
.+++||+|||
T Consensus 79 G~i~HEl~Ha 88 (182)
T cd04283 79 GIIQHELLHA 88 (182)
T ss_pred chHHHHHHHH
Confidence 4789999998
No 131
>cd06160 S2P-M50_like_2 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 additional putative N- and C-terminal transmembrane spanning regions, relative to the core protein, and no PDZ domains.
Probab=32.41 E-value=37 Score=31.02 Aligned_cols=22 Identities=27% Similarity=0.185 Sum_probs=16.5
Q ss_pred hhhhhHHHHHhHHHHhhhc-CCC
Q 016954 355 LLTGTILAHEMMHGWMRLQ-GAF 376 (380)
Q Consensus 355 ~~~g~ilahe~~ha~l~l~-g~~ 376 (380)
.+.-+|+.||++|+|.-.. |++
T Consensus 39 ~l~~~l~iHElgH~~~A~~~G~~ 61 (183)
T cd06160 39 ALLAILGIHEMGHYLAARRHGVK 61 (183)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCC
Confidence 4566889999999997544 654
No 132
>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=32.08 E-value=22 Score=38.01 Aligned_cols=13 Identities=38% Similarity=0.933 Sum_probs=11.5
Q ss_pred hhHHHHHhHHHHh
Q 016954 358 GTILAHEMMHGWM 370 (380)
Q Consensus 358 g~ilahe~~ha~l 370 (380)
+.++|||++|.|-
T Consensus 289 ~~vIaHEIAHSWt 301 (613)
T KOG1047|consen 289 VDVIAHEIAHSWT 301 (613)
T ss_pred hhHHHHHhhhhhc
Confidence 4789999999994
No 133
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=31.91 E-value=42 Score=22.96 Aligned_cols=32 Identities=31% Similarity=0.680 Sum_probs=20.7
Q ss_pred cccccCCcCCCCCceEEccCCcccChhhhhhh
Q 016954 214 RCCSCERMEPQDTAYVALDDGRKLCLECLDSA 245 (380)
Q Consensus 214 ~C~~C~r~l~~g~~f~~l~dg~~~C~~C~~~~ 245 (380)
+|+-|+|......+.+.-.++-..|..|...+
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~~ 34 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECVEQA 34 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHHHHH
Confidence 58889998876667665554777899997753
No 134
>COG5549 Predicted Zn-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=31.72 E-value=23 Score=33.29 Aligned_cols=37 Identities=22% Similarity=0.130 Sum_probs=30.7
Q ss_pred eeEEEEEEecCCChhhhhhHHHHHhHHHHhhhcCCCCC
Q 016954 341 CDVTAILILYGLPRLLTGTILAHEMMHGWMRLQGAFCL 378 (380)
Q Consensus 341 ~~v~~il~l~glp~~~~g~ilahe~~ha~l~l~g~~~l 378 (380)
.+=-+|+.-+|+-++-.-.++-||++|| |++-|+..|
T Consensus 171 nhr~~i~~~pg~~~e~L~~tarhElGha-Lgi~ghsd~ 207 (236)
T COG5549 171 NHRGDIMYPPGELRENLNPTARHELGHA-LGIWGHSDL 207 (236)
T ss_pred cccccccCCcccchhhhhHHHHHhhcch-heecccccc
Confidence 3446789999999999999999999999 777776554
No 135
>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=31.48 E-value=25 Score=39.58 Aligned_cols=13 Identities=38% Similarity=0.912 Sum_probs=11.6
Q ss_pred hhHHHHHhHHHHh
Q 016954 358 GTILAHEMMHGWM 370 (380)
Q Consensus 358 g~ilahe~~ha~l 370 (380)
..|+|||++|.|.
T Consensus 288 ~~viaHElAHqWF 300 (831)
T TIGR02412 288 AGVILHEMAHMWF 300 (831)
T ss_pred HHHHHHHHHHHHh
Confidence 4799999999996
No 136
>TIGR02289 M3_not_pepF oligoendopeptidase, M3 family. This family consists of probable oligoendopeptidases in the M3 family, related to lactococcal PepF and group B streptococcal PepB (TIGR00181) but in a distinct clade with considerable sequence differences. The likely substrate is small peptides and not whole proteins, as with PepF, but members are not characterized and the activity profile may differ. Several bacteria have both a member of this family and a member of the PepF family.
Probab=31.13 E-value=25 Score=37.47 Aligned_cols=12 Identities=33% Similarity=0.609 Sum_probs=10.1
Q ss_pred hHHHHHhHHHHh
Q 016954 359 TILAHEMMHGWM 370 (380)
Q Consensus 359 ~ilahe~~ha~l 370 (380)
.+||||++||+-
T Consensus 339 ~TL~HElGHa~H 350 (549)
T TIGR02289 339 DVLTHEAGHAFH 350 (549)
T ss_pred HHHHHHhhHHHH
Confidence 569999999973
No 137
>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=30.38 E-value=28 Score=31.77 Aligned_cols=13 Identities=23% Similarity=0.330 Sum_probs=10.4
Q ss_pred hhhHHHHHhHHHH
Q 016954 357 TGTILAHEMMHGW 369 (380)
Q Consensus 357 ~g~ilahe~~ha~ 369 (380)
.-.+++||+|||-
T Consensus 79 ~~~~i~HEl~HaL 91 (191)
T PF01400_consen 79 SVGTILHELGHAL 91 (191)
T ss_dssp SHHHHHHHHHHHH
T ss_pred CccchHHHHHHHH
Confidence 3458899999983
No 138
>PRK01265 heat shock protein HtpX; Provisional
Probab=30.06 E-value=34 Score=34.22 Aligned_cols=24 Identities=29% Similarity=0.225 Sum_probs=16.9
Q ss_pred EEEEecCC----ChhhhhhHHHHHhHHH
Q 016954 345 AILILYGL----PRLLTGTILAHEMMHG 368 (380)
Q Consensus 345 ~il~l~gl----p~~~~g~ilahe~~ha 368 (380)
.|.|-.|| .+.=..+|||||++|.
T Consensus 124 ~Ivvt~gLl~~l~~~El~aVlAHElgHi 151 (324)
T PRK01265 124 RIAITLPLLKILNRDEIKAVAGHELGHL 151 (324)
T ss_pred EEEEehHHHhhCCHHHHHHHHHHHHHHH
Confidence 35665565 4444578999999994
No 139
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=29.53 E-value=39 Score=24.21 Aligned_cols=32 Identities=13% Similarity=0.343 Sum_probs=15.6
Q ss_pred ceEEccCCcccChhhhhhhcc-CCCCCCcchHH
Q 016954 227 AYVALDDGRKLCLECLDSAIM-DTNECQPLYLD 258 (380)
Q Consensus 227 ~f~~l~dg~~~C~~C~~~~v~-~~~~C~~c~~~ 258 (380)
.|..=+=|..+|+.||..++. ....|-+|+++
T Consensus 14 ~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~ 46 (48)
T PF14570_consen 14 DFYPCECGFQICRFCYHDILENEGGRCPGCREP 46 (48)
T ss_dssp T--SSTTS----HHHHHHHTTSS-SB-TTT--B
T ss_pred ccccCcCCCcHHHHHHHHHHhccCCCCCCCCCC
Confidence 333333445679999999875 47889998853
No 140
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=29.15 E-value=32 Score=24.55 Aligned_cols=8 Identities=38% Similarity=1.128 Sum_probs=4.7
Q ss_pred cChhhhhh
Q 016954 237 LCLECLDS 244 (380)
Q Consensus 237 ~C~~C~~~ 244 (380)
+|..|+.+
T Consensus 28 lC~~C~~~ 35 (48)
T cd02341 28 LCQDCVVK 35 (48)
T ss_pred cCHHHHhC
Confidence 46666654
No 141
>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=29.12 E-value=52 Score=30.12 Aligned_cols=16 Identities=25% Similarity=0.249 Sum_probs=12.8
Q ss_pred hhhhhHHHHHhHHHHh
Q 016954 355 LLTGTILAHEMMHGWM 370 (380)
Q Consensus 355 ~~~g~ilahe~~ha~l 370 (380)
--.-+++|||+-|++.
T Consensus 63 ~~l~~~iaHE~hH~~r 78 (195)
T PF10026_consen 63 EELPALIAHEYHHNCR 78 (195)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4457899999999963
No 142
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=29.04 E-value=17 Score=29.95 Aligned_cols=28 Identities=25% Similarity=0.656 Sum_probs=18.6
Q ss_pred CcccccCCcCCCCCceEEccCCcccChhh
Q 016954 213 PRCCSCERMEPQDTAYVALDDGRKLCLEC 241 (380)
Q Consensus 213 F~C~~C~r~l~~g~~f~~l~dg~~~C~~C 241 (380)
|+|++|--.- ...+-....+|.++|..|
T Consensus 71 FTCssCFLV~-HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 71 FTCSSCFLVH-HRSQLAREKDGQPICRDC 98 (99)
T ss_pred eeeeeeeeEe-chhhhccccCCCEecccc
Confidence 8999997332 222323345899999988
No 143
>KOG3314 consensus Ku70-binding protein [Replication, recombination and repair]
Probab=28.54 E-value=32 Score=31.10 Aligned_cols=15 Identities=20% Similarity=0.583 Sum_probs=11.9
Q ss_pred hhhHHHHHhHHHHhh
Q 016954 357 TGTILAHEMMHGWMR 371 (380)
Q Consensus 357 ~g~ilahe~~ha~l~ 371 (380)
..-+++|||.|||=-
T Consensus 91 ~n~vv~HElIH~fDd 105 (194)
T KOG3314|consen 91 VNQVVIHELIHAFDD 105 (194)
T ss_pred HHHHHHHHHHHHHHh
Confidence 347899999999843
No 144
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=28.10 E-value=59 Score=38.14 Aligned_cols=13 Identities=31% Similarity=0.360 Sum_probs=7.9
Q ss_pred HHHHhHHHHhhhc
Q 016954 361 LAHEMMHGWMRLQ 373 (380)
Q Consensus 361 lahe~~ha~l~l~ 373 (380)
.||=+-||=.|-|
T Consensus 906 YAHPyFHAAKRRN 918 (1337)
T PRK14714 906 YAHPYFHAAKRRN 918 (1337)
T ss_pred cccchhhhHhhcC
Confidence 4677777655544
No 145
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 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 domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=27.99 E-value=6.9 Score=25.86 Aligned_cols=9 Identities=44% Similarity=1.180 Sum_probs=4.5
Q ss_pred ccccCCccc
Q 016954 115 ICAGCNNEI 123 (380)
Q Consensus 115 ~C~~C~~~I 123 (380)
.|..|+++|
T Consensus 5 ~C~~CGe~I 13 (36)
T PF01258_consen 5 ICEDCGEPI 13 (36)
T ss_dssp B-TTTSSBE
T ss_pred CccccCChH
Confidence 355555555
No 146
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=27.63 E-value=49 Score=22.76 Aligned_cols=8 Identities=38% Similarity=1.140 Sum_probs=5.1
Q ss_pred cChhhhhh
Q 016954 237 LCLECLDS 244 (380)
Q Consensus 237 ~C~~C~~~ 244 (380)
+|.+||.+
T Consensus 29 lC~~Cf~~ 36 (44)
T smart00291 29 LCQSCFAK 36 (44)
T ss_pred chHHHHhC
Confidence 47777654
No 147
>PF15295 CCDC50_N: Coiled-coil domain-containing protein 50 N-terminus
Probab=27.52 E-value=25 Score=30.53 Aligned_cols=41 Identities=39% Similarity=0.470 Sum_probs=28.1
Q ss_pred cchHHHHHHHhchhhhhhcCCCccCccccccchHHHHHHHHhh
Q 016954 44 ENEDIDRAIALSLLEENQKGENVIDKESQVEEDEQLARAIQES 86 (380)
Q Consensus 44 ~~e~~~~aia~sl~e~~~~~~~~~~~~~~~~edE~lar~lqes 86 (380)
+-|+.|..||..+.|+..+.... ...+.++|+.+|+.||+.
T Consensus 80 e~Ee~D~e~Ar~iqe~l~r~~e~--~r~~Ee~de~iA~~Lqe~ 120 (132)
T PF15295_consen 80 EIEEQDEEYAREIQEELQREAEE--QRQQEEEDEEIARRLQEE 120 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH--HHHHHHhhHHHHHHHHHH
Confidence 34667778888887765544332 123668999999999976
No 148
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=27.31 E-value=48 Score=22.99 Aligned_cols=8 Identities=38% Similarity=1.036 Sum_probs=4.3
Q ss_pred cChhhhhh
Q 016954 237 LCLECLDS 244 (380)
Q Consensus 237 ~C~~C~~~ 244 (380)
+|..||..
T Consensus 25 LC~~Cf~~ 32 (46)
T cd02249 25 LCSSCYAK 32 (46)
T ss_pred CHHHHHCc
Confidence 46666553
No 149
>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=27.05 E-value=32 Score=34.25 Aligned_cols=19 Identities=26% Similarity=0.371 Sum_probs=15.8
Q ss_pred cCCChhhhhhHHHHHhHHH
Q 016954 350 YGLPRLLTGTILAHEMMHG 368 (380)
Q Consensus 350 ~glp~~~~g~ilahe~~ha 368 (380)
..||....-.++||||+|.
T Consensus 189 ~~~p~~~~P~T~~HElAHq 207 (318)
T PF12725_consen 189 TDLPPYSLPFTICHELAHQ 207 (318)
T ss_pred CCCCcccccHHHHHHHHHH
Confidence 3578888889999999994
No 150
>KOG2921 consensus Intramembrane metalloprotease (sterol-regulatory element-binding protein (SREBP) protease) [Posttranslational modification, protein turnover, chaperones]
Probab=27.02 E-value=39 Score=34.73 Aligned_cols=24 Identities=29% Similarity=0.465 Sum_probs=17.9
Q ss_pred EecCCChhhhhhH---HHHHhHHHHhh
Q 016954 348 ILYGLPRLLTGTI---LAHEMMHGWMR 371 (380)
Q Consensus 348 ~l~glp~~~~g~i---lahe~~ha~l~ 371 (380)
=|-|+|..+|--| .-|||+|||-.
T Consensus 119 pl~~I~yf~t~lvi~~vvHElGHalAA 145 (484)
T KOG2921|consen 119 PLSGIAYFLTSLVITVVVHELGHALAA 145 (484)
T ss_pred ccccchhhhhhHHHHHHHHHhhHHHHH
Confidence 3567777777665 56999999954
No 151
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.89 E-value=27 Score=34.19 Aligned_cols=31 Identities=29% Similarity=0.688 Sum_probs=22.1
Q ss_pred CccccCCcccccCceEeeCCceecCCCcccC
Q 016954 114 RICAGCNNEIGHGRFLNCLDVFWHPECFCCH 144 (380)
Q Consensus 114 ~~C~~C~~~I~~g~~v~alg~~wH~~CF~C~ 144 (380)
-.|.-|++.+.+..+|.+-.-.-|.-||-|+
T Consensus 269 LcCTLC~ERLEDTHFVQCPSVp~HKFCFPCS 299 (352)
T KOG3579|consen 269 LCCTLCHERLEDTHFVQCPSVPSHKFCFPCS 299 (352)
T ss_pred eeehhhhhhhccCceeecCCCcccceecccC
Confidence 4577777777666777777777777777775
No 152
>KOG2661 consensus Peptidase family M48 [Posttranslational modification, protein turnover, chaperones]
Probab=26.87 E-value=39 Score=34.01 Aligned_cols=16 Identities=38% Similarity=0.557 Sum_probs=13.1
Q ss_pred hhhHHHHHhHHHHhhh
Q 016954 357 TGTILAHEMMHGWMRL 372 (380)
Q Consensus 357 ~g~ilahe~~ha~l~l 372 (380)
...+||||.+||-.|=
T Consensus 275 lAtvLgHE~aHaVarH 290 (424)
T KOG2661|consen 275 LATVLGHEIAHAVARH 290 (424)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3579999999998763
No 153
>PF13203 DUF2201_N: Putative metallopeptidase domain
Probab=26.77 E-value=42 Score=32.44 Aligned_cols=22 Identities=27% Similarity=0.326 Sum_probs=17.2
Q ss_pred cCCChhhhhhHHHHHhHHHHhh
Q 016954 350 YGLPRLLTGTILAHEMMHGWMR 371 (380)
Q Consensus 350 ~glp~~~~g~ilahe~~ha~l~ 371 (380)
.+|+.--...+|+||++|.-++
T Consensus 53 ~~l~~~~~~~~l~HevlH~~~~ 74 (292)
T PF13203_consen 53 ESLSPEERVGLLLHEVLHCLLR 74 (292)
T ss_pred hcCCHHHHHHHHHHHHHHHHcc
Confidence 5666666778899999998654
No 154
>COG4740 Predicted metalloprotease [General function prediction only]
Probab=26.67 E-value=44 Score=29.56 Aligned_cols=18 Identities=50% Similarity=0.612 Sum_probs=15.0
Q ss_pred EEecCCChhhhhhHHHHHhHHH
Q 016954 347 LILYGLPRLLTGTILAHEMMHG 368 (380)
Q Consensus 347 l~l~glp~~~~g~ilahe~~ha 368 (380)
|-|-|.|. +-+||||-|-
T Consensus 140 lrl~G~pA----y~~aHEleHL 157 (176)
T COG4740 140 LRLEGIPA----YNLAHELEHL 157 (176)
T ss_pred EEEecCcc----chhHHHHHHh
Confidence 67788887 7899999993
No 155
>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=26.47 E-value=31 Score=31.13 Aligned_cols=10 Identities=40% Similarity=0.813 Sum_probs=8.9
Q ss_pred hHHHHHhHHH
Q 016954 359 TILAHEMMHG 368 (380)
Q Consensus 359 ~ilahe~~ha 368 (380)
.++.||+|||
T Consensus 76 g~v~HE~~Ha 85 (180)
T cd04280 76 GTIVHELMHA 85 (180)
T ss_pred chhHHHHHHH
Confidence 5788999999
No 156
>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=26.45 E-value=55 Score=30.77 Aligned_cols=21 Identities=19% Similarity=0.245 Sum_probs=15.6
Q ss_pred ecCCChhhhhhHHHHHhHHHH
Q 016954 349 LYGLPRLLTGTILAHEMMHGW 369 (380)
Q Consensus 349 l~glp~~~~g~ilahe~~ha~ 369 (380)
+...+..+-..|++||++|+-
T Consensus 125 ~~~~~~~~~~hvi~HEiGH~I 145 (211)
T PF12388_consen 125 LSNYSVNVIEHVITHEIGHCI 145 (211)
T ss_pred cCCCchhHHHHHHHHHhhhhc
Confidence 344455667789999999973
No 157
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=26.23 E-value=43 Score=26.81 Aligned_cols=11 Identities=36% Similarity=0.773 Sum_probs=7.2
Q ss_pred cccccCCcccC
Q 016954 175 KCDVCKHFIPS 185 (380)
Q Consensus 175 kC~~C~~~I~~ 185 (380)
.|..|+.+|+.
T Consensus 2 ~C~HCg~~~p~ 12 (88)
T PF12156_consen 2 KCYHCGLPVPE 12 (88)
T ss_pred CCCCCCCCCCC
Confidence 46777777754
No 158
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=26.09 E-value=49 Score=26.17 Aligned_cols=14 Identities=14% Similarity=0.389 Sum_probs=4.9
Q ss_pred cccccccccCCccc
Q 016954 171 HYHPKCDVCKHFIP 184 (380)
Q Consensus 171 ~f~pkC~~C~~~I~ 184 (380)
+.+..|..|+..|-
T Consensus 7 ~~~qiCqiCGD~VG 20 (80)
T PF14569_consen 7 LNGQICQICGDDVG 20 (80)
T ss_dssp -SS-B-SSS--B--
T ss_pred cCCcccccccCccc
Confidence 34567888887775
No 159
>COG3590 PepO Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]
Probab=25.20 E-value=19 Score=38.51 Aligned_cols=13 Identities=38% Similarity=0.968 Sum_probs=11.7
Q ss_pred hhhHHHHHhHHHH
Q 016954 357 TGTILAHEMMHGW 369 (380)
Q Consensus 357 ~g~ilahe~~ha~ 369 (380)
-|+|.+||++|+|
T Consensus 487 IGaVIgHEI~HgF 499 (654)
T COG3590 487 IGAVIGHEIGHGF 499 (654)
T ss_pred ccceehhhhcccc
Confidence 4889999999997
No 160
>PHA02768 hypothetical protein; Provisional
Probab=25.14 E-value=23 Score=26.11 Aligned_cols=21 Identities=14% Similarity=0.496 Sum_probs=14.9
Q ss_pred CCCcccccCCcCCCCCceEEc
Q 016954 211 GTPRCCSCERMEPQDTAYVAL 231 (380)
Q Consensus 211 ~CF~C~~C~r~l~~g~~f~~l 231 (380)
.=++|..|++.+.....++.+
T Consensus 30 k~~kc~~C~k~f~~~s~l~~~ 50 (55)
T PHA02768 30 TNLKLSNCKRISLRTGEYIEI 50 (55)
T ss_pred CcccCCcccceecccceeEEE
Confidence 457899999887666666643
No 161
>COG0308 PepN Aminopeptidase N [Amino acid transport and metabolism]
Probab=25.05 E-value=49 Score=37.39 Aligned_cols=13 Identities=38% Similarity=1.022 Sum_probs=11.1
Q ss_pred hhHHHHHhHHHHh
Q 016954 358 GTILAHEMMHGWM 370 (380)
Q Consensus 358 g~ilahe~~ha~l 370 (380)
.+|.||||.|.|.
T Consensus 308 ~~viaHElaHqWf 320 (859)
T COG0308 308 EEVIAHELAHQWF 320 (859)
T ss_pred HHHHHHHHhhhcc
Confidence 3499999999994
No 162
>COG5148 RPN10 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=24.98 E-value=25 Score=32.50 Aligned_cols=33 Identities=30% Similarity=0.463 Sum_probs=21.1
Q ss_pred chHHHHHHHhchhhhhhcCCCccCccccccchH
Q 016954 45 NEDIDRAIALSLLEENQKGENVIDKESQVEEDE 77 (380)
Q Consensus 45 ~e~~~~aia~sl~e~~~~~~~~~~~~~~~~edE 77 (380)
+.++.-||.||+.|+.++.+...-..++.++|+
T Consensus 207 DpELA~AlrLSmeEek~rQe~~~qk~~ee~e~~ 239 (243)
T COG5148 207 DPELAEALRLSMEEEKKRQEVAAQKSSEETEDK 239 (243)
T ss_pred CHHHHHHHHhhHHHHHHHHHHHHHhhhhccchh
Confidence 557888999999888776655433333333333
No 163
>PHA00527 hypothetical protein
Probab=24.77 E-value=1e+02 Score=25.77 Aligned_cols=13 Identities=31% Similarity=0.342 Sum_probs=10.4
Q ss_pred hhHHHHHhHHHHh
Q 016954 358 GTILAHEMMHGWM 370 (380)
Q Consensus 358 g~ilahe~~ha~l 370 (380)
-|.||||++|+=.
T Consensus 74 ~~T~~HECAH~AF 86 (129)
T PHA00527 74 AATLVHECAHVAF 86 (129)
T ss_pred HHHHHHHHHHHHH
Confidence 3789999999744
No 164
>PF10462 Peptidase_M66: Peptidase M66; InterPro: IPR019503 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 is a family of metallopeptidases belonging to MEROPS peptidase family M66 (StcE peptidase, clan MA). The StcE peptidase is a virulence factor found in Shiga toxigenic Escherichia coli strains. StcE peptidase cleaves C1 esterase inhibitor []. The SwissProt proteins in this entry have been name "Dictomallein". ; GO: 0004222 metalloendopeptidase activity; PDB: 3UJZ_A.
Probab=24.59 E-value=35 Score=33.81 Aligned_cols=14 Identities=29% Similarity=0.501 Sum_probs=12.4
Q ss_pred hhhHHHHHhHHHHh
Q 016954 357 TGTILAHEMMHGWM 370 (380)
Q Consensus 357 ~g~ilahe~~ha~l 370 (380)
.|.+++||++|+|=
T Consensus 193 ~~~~f~HE~GH~~G 206 (305)
T PF10462_consen 193 YGNEFSHELGHNFG 206 (305)
T ss_dssp SHHHHHHHHHHTTT
T ss_pred ccceeehhhhhhcC
Confidence 58999999999983
No 165
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 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. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=24.51 E-value=37 Score=24.37 Aligned_cols=43 Identities=21% Similarity=0.420 Sum_probs=24.6
Q ss_pred CcccccCCcCCCCCceEEccCCcccChhhhhhhccCCCCCCcchHHH
Q 016954 213 PRCCSCERMEPQDTAYVALDDGRKLCLECLDSAIMDTNECQPLYLDI 259 (380)
Q Consensus 213 F~C~~C~r~l~~g~~f~~l~dg~~~C~~C~~~~v~~~~~C~~c~~~I 259 (380)
|.|.+|- + .....+. -.++-+|+.|...+...++.|.-|++++
T Consensus 3 ~nCKsCW--f-~~k~Li~-C~dHYLCl~CLt~ml~~s~~C~iC~~~L 45 (50)
T PF03854_consen 3 YNCKSCW--F-ANKGLIK-CSDHYLCLNCLTLMLSRSDRCPICGKPL 45 (50)
T ss_dssp ----SS---S---SSEEE--SS-EEEHHHHHHT-SSSSEETTTTEE-
T ss_pred ccChhhh--h-cCCCeee-ecchhHHHHHHHHHhccccCCCcccCcC
Confidence 4677887 4 3444553 3567889999998877888999988554
No 166
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=24.22 E-value=44 Score=33.31 Aligned_cols=20 Identities=25% Similarity=0.296 Sum_probs=15.0
Q ss_pred CCCccccCCcccccCceEee
Q 016954 112 GYRICAGCNNEIGHGRFLNC 131 (380)
Q Consensus 112 ~~~~C~~C~~~I~~g~~v~a 131 (380)
+.-.|..|+..|+.|..+++
T Consensus 39 f~i~C~~C~~~I~kG~rFNA 58 (324)
T PF04502_consen 39 FNIWCNTCGEYIYKGVRFNA 58 (324)
T ss_pred ccCcCCCCccccccceeeee
Confidence 55778888888877766665
No 167
>cd06459 M3B_Oligoendopeptidase_F Peptidase family M3B Oligopeptidase F (PepF; Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and includes oligoendopeptidase F from Lactococcus lactis. This enzyme hydrolyzes peptides containing between 7 and 17 amino acids with fairly broad specificity. The PepF gene is duplicated in L. lactis on the plasmid that bears it, while a shortened second copy is found in Bacillus subtilis. Most bacterial PepFs are cytoplasmic endopeptidases; however, the PepF Bacillus amyloliquefaciens oligopeptidase is a secreted protein and may facilitate the process of sporulation. Specifically, the yjbG gene encoding the homolog of the PepF1 and PepF2 oligoendopeptidases of Lactococcus lactis has been identified in Bacillus subtilis as an inhibitor of sporulation initiation when over expressed from a multicopy plasmid.
Probab=23.34 E-value=42 Score=33.95 Aligned_cols=13 Identities=38% Similarity=0.542 Sum_probs=10.1
Q ss_pred hHHHHHhHHHHhh
Q 016954 359 TILAHEMMHGWMR 371 (380)
Q Consensus 359 ~ilahe~~ha~l~ 371 (380)
..|+||++||+--
T Consensus 224 ~tl~HE~GHa~h~ 236 (427)
T cd06459 224 FTLAHELGHAFHS 236 (427)
T ss_pred HHHHHHhhHHHHH
Confidence 4599999998643
No 168
>TIGR02290 M3_fam_3 oligoendopeptidase, pepF/M3 family. The M3 family of metallopeptidases contains several distinct clades. Oligoendopeptidase F as characterized in Lactococcus, the functionally equivalent oligoendopeptidase B of group B Streptococcus, and closely related sequences are described by TIGR00181. The present family is quite similar but forms a distinct clade, and a number of species have one member of each. A greater sequence difference separates members of TIGR02289, probable oligoendopeptidases of the M3 family that probably should not be designated PepF.
Probab=23.24 E-value=41 Score=36.06 Aligned_cols=11 Identities=45% Similarity=0.812 Sum_probs=9.6
Q ss_pred hHHHHHhHHHH
Q 016954 359 TILAHEMMHGW 369 (380)
Q Consensus 359 ~ilahe~~ha~ 369 (380)
..||||++||+
T Consensus 377 ~TL~HE~GHa~ 387 (587)
T TIGR02290 377 STLAHELGHAY 387 (587)
T ss_pred HHHHHHhhHHH
Confidence 45999999998
No 169
>PF02031 Peptidase_M7: Streptomyces extracellular neutral proteinase (M7) family; InterPro: IPR000013 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 M7 (snapalysin 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. With a molecular weight of around 16kDa, Streptomyces extracellular neutral protease is one of the smallest known proteases []; it is capable of hydrolysing milk proteins []. The enzyme is synthesised as a proenzyme with a signal peptide, a propeptide and an active domain that contains the conserved HEXXH motif characteristic of metalloproteases. Although family M7 shows active site sequence similarity to other members, it differs in one major respect: the third zinc ligand appears to be an aspartate residue rather than the usual histidine.; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis, 0005576 extracellular region; PDB: 1C7K_A 1KUH_A.
Probab=23.16 E-value=46 Score=28.90 Aligned_cols=9 Identities=56% Similarity=0.578 Sum_probs=8.5
Q ss_pred HHHHHhHHH
Q 016954 360 ILAHEMMHG 368 (380)
Q Consensus 360 ilahe~~ha 368 (380)
|.|||++|.
T Consensus 80 IaaHE~GHi 88 (132)
T PF02031_consen 80 IAAHELGHI 88 (132)
T ss_dssp HHHHHHHHH
T ss_pred eeeehhccc
Confidence 999999997
No 170
>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=22.78 E-value=14 Score=34.02 Aligned_cols=14 Identities=36% Similarity=0.427 Sum_probs=11.6
Q ss_pred hhhhhHHHHHhHHH
Q 016954 355 LLTGTILAHEMMHG 368 (380)
Q Consensus 355 ~~~g~ilahe~~ha 368 (380)
+.++.|+|||++|.
T Consensus 138 ~~~a~~~aHElGH~ 151 (207)
T cd04273 138 LSSAFTIAHELGHV 151 (207)
T ss_pred ceeEEeeeeechhh
Confidence 45678999999995
No 171
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=22.60 E-value=70 Score=22.56 Aligned_cols=8 Identities=63% Similarity=1.589 Sum_probs=4.2
Q ss_pred cChhhhhh
Q 016954 237 LCLECLDS 244 (380)
Q Consensus 237 ~C~~C~~~ 244 (380)
+|..||..
T Consensus 26 LC~~Cf~~ 33 (49)
T cd02335 26 LCLECFSA 33 (49)
T ss_pred hhHHhhhC
Confidence 45555553
No 172
>PRK04023 DNA polymerase II large subunit; Validated
Probab=22.51 E-value=90 Score=35.85 Aligned_cols=38 Identities=18% Similarity=0.246 Sum_probs=22.3
Q ss_pred cccCCCCCCCCCceeeccCCcccccccccccccccccccCCcccCC
Q 016954 141 FCCHACHQPITDIEFSTSENRPYHKSCYREHYHPKCDVCKHFIPSN 186 (380)
Q Consensus 141 F~C~~C~~~L~~~~f~~~dg~~YC~~cy~~~f~pkC~~C~~~I~~~ 186 (380)
|+|..|+.. ......|..|-.......|..|+..+.+.
T Consensus 639 frCP~CG~~--------Te~i~fCP~CG~~~~~y~CPKCG~El~~~ 676 (1121)
T PRK04023 639 RRCPFCGTH--------TEPVYRCPRCGIEVEEDECEKCGREPTPY 676 (1121)
T ss_pred ccCCCCCCC--------CCcceeCccccCcCCCCcCCCCCCCCCcc
Confidence 667777665 12223566775555455677777766654
No 173
>PRK00420 hypothetical protein; Validated
Probab=22.50 E-value=53 Score=27.78 Aligned_cols=10 Identities=0% Similarity=-0.114 Sum_probs=5.1
Q ss_pred cCCccccccc
Q 016954 158 SENRPYHKSC 167 (380)
Q Consensus 158 ~dg~~YC~~c 167 (380)
.+|+.||..|
T Consensus 37 k~g~~~Cp~C 46 (112)
T PRK00420 37 KDGEVVCPVH 46 (112)
T ss_pred CCCceECCCC
Confidence 4555555443
No 174
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=22.46 E-value=78 Score=22.24 Aligned_cols=30 Identities=23% Similarity=0.559 Sum_probs=16.9
Q ss_pred cccccCCcCCCCCceEEccC-CcccChhhhhh
Q 016954 214 RCCSCERMEPQDTAYVALDD-GRKLCLECLDS 244 (380)
Q Consensus 214 ~C~~C~r~l~~g~~f~~l~d-g~~~C~~C~~~ 244 (380)
.|.+|+.-.+ ..+|..++. ..-+|..||.+
T Consensus 2 ~C~~Cg~D~t-~vryh~~~~~~~dLC~~CF~~ 32 (45)
T cd02336 2 HCFTCGNDCT-RVRYHNLKAKKYDLCPSCYQE 32 (45)
T ss_pred cccCCCCccC-ceEEEecCCCccccChHHHhC
Confidence 4677776553 345543332 24567777765
No 175
>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=22.37 E-value=32 Score=32.41 Aligned_cols=11 Identities=36% Similarity=0.745 Sum_probs=9.5
Q ss_pred hHHHHHhHHHH
Q 016954 359 TILAHEMMHGW 369 (380)
Q Consensus 359 ~ilahe~~ha~ 369 (380)
.++||||+|-.
T Consensus 147 ~t~AHElGHnL 157 (228)
T cd04271 147 QVFAHEIGHTF 157 (228)
T ss_pred eehhhhhhhhc
Confidence 69999999964
No 176
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=22.29 E-value=1.2e+02 Score=29.75 Aligned_cols=92 Identities=16% Similarity=0.215 Sum_probs=45.8
Q ss_pred CCCCCCC---CCCCCCCCCCCcchHHHHHHHhchhhhhhcCCCccCccccccchHHHHHHHHhhcCCCCCCCCCCCCccc
Q 016954 26 EDPHCYA---PSTSGDLPLEQENEDIDRAIALSLLEENQKGENVIDKESQVEEDEQLARAIQESLNLESPPRQGTAHTYQ 102 (380)
Q Consensus 26 ~~~~~~~---~~~~~~~~~~~~~e~~~~aia~sl~e~~~~~~~~~~~~~~~~edE~lar~lqes~~~~sppr~~~~~~~~ 102 (380)
+.+.|.+ |.++.++-++.+.+.+-.||..-|++.-..+......-.+ ..+...-|+
T Consensus 177 ~E~Lf~agI~P~~~a~~l~~~~~~~l~~~i~~vl~~ai~~gGtt~r~~~~---------------------~~g~~G~fq 235 (273)
T COG0266 177 DEILFRAGIHPARPAGDLSLAQLALLHEAIKDVLADAIERGGTTLRDFVN---------------------ADGKPGYFQ 235 (273)
T ss_pred HHHHHHcCCCcccCccccCHHHHHHHHHHHHHHHHHHHHhCCCcccceec---------------------cCCCCCccc
Confidence 4455554 5555566666666666667766665544433321110000 000112233
Q ss_pred CCCccCCCCCCCccccCCcccccCceEeeCCceecCCC
Q 016954 103 HFPVIQFPEGYRICAGCNNEIGHGRFLNCLDVFWHPEC 140 (380)
Q Consensus 103 p~~~~~~~~~~~~C~~C~~~I~~g~~v~alg~~wH~~C 140 (380)
... .-+-.....|.+|+.+| ....+.-.+..|-|.|
T Consensus 236 ~~l-~VYgR~GepC~~CGt~I-~k~~~~gR~t~~CP~C 271 (273)
T COG0266 236 QEL-KVYGRAGEPCRRCGTPI-EKIKLGGRSTFYCPVC 271 (273)
T ss_pred eeE-EEecCCCCCCCccCCEe-EEEEEcCCcCEeCCCC
Confidence 321 11333556799999999 4445555556664444
No 177
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=22.22 E-value=31 Score=26.72 Aligned_cols=38 Identities=16% Similarity=0.390 Sum_probs=17.0
Q ss_pred ccCCCCCCCCCceeeccCCccccccccccc-ccccccccCCccc
Q 016954 142 CCHACHQPITDIEFSTSENRPYHKSCYREH-YHPKCDVCKHFIP 184 (380)
Q Consensus 142 ~C~~C~~~L~~~~f~~~dg~~YC~~cy~~~-f~pkC~~C~~~I~ 184 (380)
.|..|+.+|.. .++..+|..|-... ..+.|..|++++.
T Consensus 3 ~CP~C~~~L~~-----~~~~~~C~~C~~~~~~~a~CPdC~~~Le 41 (70)
T PF07191_consen 3 TCPKCQQELEW-----QGGHYHCEACQKDYKKEAFCPDCGQPLE 41 (70)
T ss_dssp B-SSS-SBEEE-----ETTEEEETTT--EEEEEEE-TTT-SB-E
T ss_pred cCCCCCCccEE-----eCCEEECccccccceecccCCCcccHHH
Confidence 35556555543 23555566554321 2467888888775
No 178
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=21.99 E-value=39 Score=30.21 Aligned_cols=53 Identities=21% Similarity=0.380 Sum_probs=34.4
Q ss_pred CCCccccCCcccccCceEeeCCceecCCCcccCCCCCCCCCceeeccCCcccccccccccccccccccCCccc
Q 016954 112 GYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREHYHPKCDVCKHFIP 184 (380)
Q Consensus 112 ~~~~C~~C~~~I~~g~~v~alg~~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~cy~~~f~pkC~~C~~~I~ 184 (380)
...-|.+||.... -.|..|+.+|.+. +..+|.++-..+|. --..|..|+++.+
T Consensus 27 ~~~fC~kCG~~tI----------------~~Cp~C~~~IrG~--y~v~gv~~~g~~~~--~PsYC~~CGkpyP 79 (158)
T PF10083_consen 27 REKFCSKCGAKTI----------------TSCPNCSTPIRGD--YHVEGVFGLGGHYE--APSYCHNCGKPYP 79 (158)
T ss_pred HHHHHHHhhHHHH----------------HHCcCCCCCCCCc--eecCCeeeeCCCCC--CChhHHhCCCCCc
Confidence 3456888887653 3678888888764 23455555455554 1347999999876
No 179
>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=21.89 E-value=1e+02 Score=31.71 Aligned_cols=17 Identities=29% Similarity=0.241 Sum_probs=13.0
Q ss_pred hhHHHHHhHHHHhhhcC
Q 016954 358 GTILAHEMMHGWMRLQG 374 (380)
Q Consensus 358 g~ilahe~~ha~l~l~g 374 (380)
-..|+||++||+--+-.
T Consensus 243 v~tLfHE~GHa~H~~ls 259 (458)
T PF01432_consen 243 VETLFHEFGHAMHSLLS 259 (458)
T ss_dssp HHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHhHHHHHHHh
Confidence 35699999999866543
No 180
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=21.86 E-value=59 Score=19.89 Aligned_cols=11 Identities=27% Similarity=0.688 Sum_probs=7.0
Q ss_pred ccccCCcccCC
Q 016954 176 CDVCKHFIPSN 186 (380)
Q Consensus 176 C~~C~~~I~~~ 186 (380)
|..|+..|.+.
T Consensus 1 C~sC~~~i~~r 11 (24)
T PF07754_consen 1 CTSCGRPIAPR 11 (24)
T ss_pred CccCCCcccCc
Confidence 56677777653
No 181
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=21.63 E-value=25 Score=32.71 Aligned_cols=40 Identities=23% Similarity=0.581 Sum_probs=0.0
Q ss_pred cccCCCCCCCCCceeeccCCcccccccccccc--cccccccCC
Q 016954 141 FCCHACHQPITDIEFSTSENRPYHKSCYREHY--HPKCDVCKH 181 (380)
Q Consensus 141 F~C~~C~~~L~~~~f~~~dg~~YC~~cy~~~f--~pkC~~C~~ 181 (380)
|.|..|.+.... ..+..=|..+|..|+...+ ++.|.+|++
T Consensus 197 F~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk 238 (259)
T COG5152 197 FLCGICKKDYES-PVVTECGHSFCSLCAIRKYQKGDECGVCGK 238 (259)
T ss_pred eeehhchhhccc-hhhhhcchhHHHHHHHHHhccCCcceecch
No 182
>KOG2719 consensus Metalloprotease [General function prediction only]
Probab=21.57 E-value=44 Score=34.62 Aligned_cols=15 Identities=33% Similarity=0.164 Sum_probs=11.7
Q ss_pred hhhhhHHHHHhHHHH
Q 016954 355 LLTGTILAHEMMHGW 369 (380)
Q Consensus 355 ~~~g~ilahe~~ha~ 369 (380)
.-.-+|||||++|--
T Consensus 278 eel~AVl~HELGHW~ 292 (428)
T KOG2719|consen 278 EELVAVLAHELGHWK 292 (428)
T ss_pred HHHHHHHHHHhhHHH
Confidence 345689999999953
No 183
>PF11571 Med27: Mediator complex subunit 27; InterPro: IPR021627 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells [].
Probab=21.52 E-value=35 Score=27.39 Aligned_cols=17 Identities=24% Similarity=0.825 Sum_probs=14.7
Q ss_pred cccccccccccccCCcc
Q 016954 167 CYREHYHPKCDVCKHFI 183 (380)
Q Consensus 167 cy~~~f~pkC~~C~~~I 183 (380)
-|..+|..+|..|++.+
T Consensus 48 sY~~lfs~pC~~C~klL 64 (90)
T PF11571_consen 48 SYRNLFSTPCKKCGKLL 64 (90)
T ss_pred HHhhhccchhhHHHhHh
Confidence 36778999999999998
No 184
>TIGR02890 spore_yteA sporulation protein, yteA family. Members of this predicted regulatory protein are found only in endospore-forming members of the Firmicutes group of bacteria, and in nearly every such species; Clostridium perfringens seems to be an exception. The member from Bacillus subtilis, the model system for the study of the sporulation program, has been designated both yteA and yzwB. Some (but not all) members of this family show a strong sequence match to PFAM family pfam01258 the C4-type zinc finger protein, DksA/TraR family, but only one of the four key Cys residues is conserved. All members of this protein family share an additional C-terminal domain. The function of proteins in this family is unknown. YteA was detected in mature spores of Bacillus subtilis by Kuwana, et al., and appears to be expressed under control of sigma-K.
Probab=21.26 E-value=32 Score=30.81 Aligned_cols=32 Identities=28% Similarity=0.606 Sum_probs=19.0
Q ss_pred CCCCccccCCcccccCceEeeCCceecCCCcccCCCCC
Q 016954 111 EGYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQ 148 (380)
Q Consensus 111 ~~~~~C~~C~~~I~~g~~v~alg~~wH~~CF~C~~C~~ 148 (380)
.....|..|+.+|.. ..+.+ -|..-.|..|..
T Consensus 84 G~YG~Ce~CGe~I~~-~RL~a-----~P~a~~Ci~Cq~ 115 (159)
T TIGR02890 84 GTYGICEVCGKPIPY-ERLEA-----IPTATTCVECQN 115 (159)
T ss_pred CCCCeecccCCcccH-HHHhh-----CCCcchhHHHHH
Confidence 356799999999943 33333 234445555533
No 185
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=20.83 E-value=67 Score=31.99 Aligned_cols=13 Identities=31% Similarity=0.634 Sum_probs=8.4
Q ss_pred ccccccccCCccc
Q 016954 172 YHPKCDVCKHFIP 184 (380)
Q Consensus 172 f~pkC~~C~~~I~ 184 (380)
|.-+|..|...|.
T Consensus 76 F~~kC~~C~~~i~ 88 (324)
T PF04502_consen 76 FYIKCPRCSNEIE 88 (324)
T ss_pred EEEEcCCCCCEEe
Confidence 5566777776654
No 186
>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=20.73 E-value=53 Score=29.45 Aligned_cols=16 Identities=19% Similarity=0.160 Sum_probs=12.5
Q ss_pred hhhhhhHHHHHhHHHH
Q 016954 354 RLLTGTILAHEMMHGW 369 (380)
Q Consensus 354 ~~~~g~ilahe~~ha~ 369 (380)
.-..-.++.||++||-
T Consensus 110 g~~~~~t~~HEiGHaL 125 (186)
T cd04277 110 GSYGYQTIIHEIGHAL 125 (186)
T ss_pred ChhhHHHHHHHHHHHh
Confidence 3455688999999983
No 187
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=20.41 E-value=76 Score=33.49 Aligned_cols=41 Identities=20% Similarity=0.396 Sum_probs=27.8
Q ss_pred CCCccccCCcccccCceEeeCCceecCCCcccCCCCCCCCCc
Q 016954 112 GYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDI 153 (380)
Q Consensus 112 ~~~~C~~C~~~I~~g~~v~alg~~wH~~CF~C~~C~~~L~~~ 153 (380)
..-.|..|-..+ +..-+...+..-...||.|..|..+|+-.
T Consensus 25 ~~~yCp~CL~~~-p~~e~~~~~nrC~r~Cf~CP~C~~~L~~~ 65 (483)
T PF05502_consen 25 DSYYCPNCLFEV-PSSEARSEKNRCSRNCFDCPICFSPLSVR 65 (483)
T ss_pred ceeECccccccC-ChhhheeccceeccccccCCCCCCcceeE
Confidence 345577787776 33334444555566899999999988753
No 188
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=20.34 E-value=30 Score=33.73 Aligned_cols=90 Identities=13% Similarity=0.221 Sum_probs=0.0
Q ss_pred CCCCCccccCCcccccCceEeeCCceecCCCcccCCCCCCCC-----CceeeccCCcccccccccccccc-cccccCCcc
Q 016954 110 PEGYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPIT-----DIEFSTSENRPYHKSCYREHYHP-KCDVCKHFI 183 (380)
Q Consensus 110 ~~~~~~C~~C~~~I~~g~~v~alg~~wH~~CF~C~~C~~~L~-----~~~f~~~dg~~YC~~cy~~~f~p-kC~~C~~~I 183 (380)
......|.-|++.- ...-...|-..-|.-=+.|..||+.++ +.-+-.+.|. .| .|..|++..
T Consensus 158 s~ka~~C~~C~K~Y-vSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGE-----------KPF~C~hC~kAF 225 (279)
T KOG2462|consen 158 SKKAFSCKYCGKVY-VSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGE-----------KPFSCPHCGKAF 225 (279)
T ss_pred ccccccCCCCCcee-eehHHHhhHhhccCCCcccccccccccchHHhhcccccccCC-----------CCccCCcccchh
Q ss_pred cCCCCcceEEecccccccccCCCCccCCCCcccccCCcC
Q 016954 184 PSNHGGLIEYRAHPFWVQKYCPSHEHDGTPRCCSCERME 222 (380)
Q Consensus 184 ~~~~~~~i~~~~~~fw~qkycp~h~H~~CF~C~~C~r~l 222 (380)
.+..+-.-....|. ++.=|.|..|+|.|
T Consensus 226 ADRSNLRAHmQTHS-----------~~K~~qC~~C~KsF 253 (279)
T KOG2462|consen 226 ADRSNLRAHMQTHS-----------DVKKHQCPRCGKSF 253 (279)
T ss_pred cchHHHHHHHHhhc-----------CCccccCcchhhHH
No 189
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.21 E-value=83 Score=31.27 Aligned_cols=28 Identities=21% Similarity=0.488 Sum_probs=16.7
Q ss_pred cCCcccChhhhhhhcc-CCCCCCcchHHH
Q 016954 232 DDGRKLCLECLDSAIM-DTNECQPLYLDI 259 (380)
Q Consensus 232 ~dg~~~C~~C~~~~v~-~~~~C~~c~~~I 259 (380)
.=|+.+|..|.+.+.. ....|..|...+
T Consensus 25 ~CGH~~C~sCv~~l~~~~~~~CP~C~~~l 53 (309)
T TIGR00570 25 VCGHTLCESCVDLLFVRGSGSCPECDTPL 53 (309)
T ss_pred CCCCcccHHHHHHHhcCCCCCCCCCCCcc
Confidence 3467777777776543 334677775444
No 190
>PLN02195 cellulose synthase A
Probab=20.02 E-value=80 Score=36.12 Aligned_cols=53 Identities=28% Similarity=0.621 Sum_probs=33.6
Q ss_pred CCCCccccCCcccccCceEeeCCceecCCCcccCCCCCCCCCceeeccCCccccccccccc---ccccccccCCccc
Q 016954 111 EGYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREH---YHPKCDVCKHFIP 184 (380)
Q Consensus 111 ~~~~~C~~C~~~I~~g~~v~alg~~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC~~cy~~~---f~pkC~~C~~~I~ 184 (380)
++..+|.-|+..|+ +..+|..| -.|..|+- |.|+.||+-. -...|..|+..-.
T Consensus 4 ~~~~~c~~cgd~~~----~~~~g~~f----vaC~eC~~-------------pvCrpCyeyer~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 4 SGAPICATCGEEVG----VDSNGEAF----VACHECSY-------------PLCKACLEYEIKEGRKVCLRCGGPYD 59 (977)
T ss_pred CCCccceecccccC----cCCCCCeE----EEeccCCC-------------ccccchhhhhhhcCCccCCccCCccc
Confidence 35678999999885 33555554 34566643 4577777421 2346778887766
Done!