Query 019740
Match_columns 336
No_of_seqs 332 out of 1309
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 04:10:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019740.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019740hhsearch_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 1.8E-77 4E-82 536.3 15.0 194 134-335 1-194 (212)
2 KOG2272 Focal adhesion protein 99.9 7.5E-26 1.6E-30 207.1 1.2 153 2-185 33-254 (332)
3 KOG1703 Adaptor protein Enigma 99.9 8.5E-24 1.8E-28 214.9 8.2 302 9-335 151-456 (479)
4 KOG1701 Focal adhesion adaptor 99.8 1.9E-22 4.2E-27 196.2 -4.7 145 1-176 294-438 (468)
5 KOG1701 Focal adhesion adaptor 99.7 3.5E-18 7.6E-23 166.7 5.4 103 1-114 352-462 (468)
6 KOG4577 Transcription factor L 99.6 4.8E-17 1E-21 151.8 -2.8 101 1-114 52-153 (383)
7 KOG1044 Actin-binding LIM Zn-f 99.5 1.8E-15 3.9E-20 152.2 2.3 192 2-235 35-246 (670)
8 KOG1703 Adaptor protein Enigma 99.5 3.3E-15 7.1E-20 152.2 3.6 153 1-179 322-477 (479)
9 KOG2272 Focal adhesion protein 99.5 1.8E-15 3.9E-20 139.2 -1.2 99 1-113 213-311 (332)
10 KOG1044 Actin-binding LIM Zn-f 99.4 5.5E-14 1.2E-18 141.6 1.2 97 1-112 152-248 (670)
11 PF00412 LIM: LIM domain; Int 98.9 5.2E-10 1.1E-14 81.2 0.9 41 1-41 18-58 (58)
12 PF00412 LIM: LIM domain; Int 98.8 9.8E-09 2.1E-13 74.5 4.4 56 45-113 1-56 (58)
13 KOG1700 Regulatory protein MLP 98.5 3.3E-08 7E-13 90.2 0.4 98 2-113 27-165 (200)
14 smart00132 LIM Zinc-binding do 97.5 6.4E-05 1.4E-09 49.4 2.6 38 44-92 1-38 (39)
15 KOG4577 Transcription factor L 97.5 2.8E-06 6E-11 80.3 -5.8 76 36-128 27-102 (383)
16 smart00132 LIM Zinc-binding do 97.0 0.00035 7.5E-09 45.8 1.2 20 1-20 19-38 (39)
17 KOG0490 Transcription factor, 96.5 0.00032 6.9E-09 64.1 -2.3 99 2-113 16-118 (235)
18 PF13485 Peptidase_MA_2: Pepti 95.7 0.022 4.8E-07 46.1 5.2 43 220-262 19-63 (128)
19 KOG1702 Nebulin repeat protein 94.7 0.0068 1.5E-07 55.3 -0.8 40 1-40 23-62 (264)
20 KOG1700 Regulatory protein MLP 94.4 0.016 3.5E-07 53.0 1.0 40 2-41 128-167 (200)
21 PF04450 BSP: Peptidase of pla 86.5 0.63 1.4E-05 42.8 3.1 38 224-262 94-131 (205)
22 PF14891 Peptidase_M91: Effect 82.1 0.9 2E-05 40.4 2.1 20 225-244 102-121 (174)
23 PF10026 DUF2268: Predicted Zn 81.4 2.1 4.5E-05 38.7 4.2 45 224-268 63-113 (195)
24 PF01433 Peptidase_M1: Peptida 81.4 0.74 1.6E-05 45.1 1.4 43 226-268 295-339 (390)
25 PF01431 Peptidase_M13: Peptid 79.7 0.68 1.5E-05 41.7 0.5 17 225-241 35-51 (206)
26 PF06114 DUF955: Domain of unk 78.3 2.4 5.2E-05 33.6 3.3 52 213-264 29-86 (122)
27 PF10263 SprT-like: SprT-like 77.2 1.5 3.3E-05 37.6 1.9 22 221-242 55-76 (157)
28 KOG0320 Predicted E3 ubiquitin 74.4 1.1 2.3E-05 40.4 0.2 49 7-55 129-180 (187)
29 PF13699 DUF4157: Domain of un 74.0 2 4.4E-05 33.4 1.7 18 226-243 61-78 (79)
30 PF14835 zf-RING_6: zf-RING of 73.3 3.4 7.4E-05 31.1 2.6 47 10-56 8-54 (65)
31 PF10460 Peptidase_M30: Peptid 71.8 4.5 9.8E-05 40.4 3.9 41 225-265 138-184 (366)
32 PF10367 Vps39_2: Vacuolar sor 71.7 2.8 6E-05 33.4 2.0 29 11-39 80-109 (109)
33 PF08394 Arc_trans_TRASH: Arch 71.2 1.1 2.5E-05 30.0 -0.3 33 45-91 1-33 (37)
34 smart00731 SprT SprT homologue 70.1 3.3 7.1E-05 35.6 2.2 23 221-243 54-76 (146)
35 KOG1702 Nebulin repeat protein 69.3 0.59 1.3E-05 42.9 -2.6 58 43-114 5-62 (264)
36 TIGR02412 pepN_strep_liv amino 69.2 4.7 0.0001 44.4 3.8 40 227-266 288-329 (831)
37 PRK14559 putative protein seri 66.8 5.8 0.00012 42.6 3.7 38 11-55 3-40 (645)
38 PF07191 zinc-ribbons_6: zinc- 65.4 3.7 8E-05 31.5 1.4 57 11-92 3-61 (70)
39 KOG1813 Predicted E3 ubiquitin 63.3 3.9 8.5E-05 39.6 1.4 45 10-55 242-288 (313)
40 PF09768 Peptidase_M76: Peptid 61.7 4.5 9.8E-05 36.3 1.5 19 223-241 68-86 (173)
41 PF01447 Peptidase_M4: Thermol 61.7 4.9 0.00011 35.1 1.7 18 222-239 131-148 (150)
42 smart00504 Ubox Modified RING 60.3 5.6 0.00012 28.5 1.5 45 10-55 2-48 (63)
43 PRK14890 putative Zn-ribbon RN 60.0 5.5 0.00012 29.5 1.4 37 11-51 9-45 (59)
44 COG2856 Predicted Zn peptidase 59.9 16 0.00035 33.8 4.8 55 213-267 59-120 (213)
45 PRK04351 hypothetical protein; 59.6 6.8 0.00015 34.2 2.2 22 222-243 57-78 (149)
46 COG1645 Uncharacterized Zn-fin 59.3 5.1 0.00011 34.4 1.3 23 11-38 30-52 (131)
47 PF13920 zf-C3HC4_3: Zinc fing 59.0 5.2 0.00011 27.8 1.1 43 11-54 4-49 (50)
48 PF12773 DZR: Double zinc ribb 58.8 9.3 0.0002 26.5 2.4 11 104-114 29-39 (50)
49 cd04270 ZnMc_TACE_like Zinc-de 58.1 5.7 0.00012 37.2 1.6 18 221-238 162-179 (244)
50 PF01435 Peptidase_M48: Peptid 58.0 8.2 0.00018 34.6 2.6 29 214-242 73-105 (226)
51 PF10367 Vps39_2: Vacuolar sor 57.0 8.9 0.00019 30.4 2.4 27 84-111 81-107 (109)
52 PF14471 DUF4428: Domain of un 57.0 3.4 7.4E-05 29.6 -0.1 29 11-40 1-30 (51)
53 PF06677 Auto_anti-p27: Sjogre 56.0 7.4 0.00016 26.6 1.5 22 11-36 19-40 (41)
54 PHA02456 zinc metallopeptidase 53.8 7.8 0.00017 32.5 1.5 17 228-244 81-98 (141)
55 PF14446 Prok-RING_1: Prokaryo 53.2 8.1 0.00017 28.1 1.3 39 11-51 7-50 (54)
56 PF14634 zf-RING_5: zinc-RING 52.9 7.4 0.00016 26.4 1.1 39 12-50 2-44 (44)
57 KOG0320 Predicted E3 ubiquitin 52.7 6.2 0.00013 35.6 0.8 51 78-129 128-178 (187)
58 PF14471 DUF4428: Domain of un 52.4 8.5 0.00019 27.5 1.4 30 83-114 1-30 (51)
59 PF10083 DUF2321: Uncharacteri 52.3 5.2 0.00011 35.2 0.3 54 29-95 27-82 (158)
60 PF01421 Reprolysin: Reprolysi 50.5 15 0.00033 32.8 3.0 24 214-237 119-142 (199)
61 PF11781 RRN7: RNA polymerase 50.2 8.3 0.00018 25.6 0.9 26 10-39 9-34 (36)
62 PF01258 zf-dskA_traR: Prokary 48.1 1.9 4.1E-05 28.3 -2.4 28 12-39 6-33 (36)
63 cd00162 RING RING-finger (Real 48.0 5.9 0.00013 25.5 -0.0 40 12-51 2-44 (45)
64 PF02163 Peptidase_M50: Peptid 47.8 14 0.00031 32.6 2.4 21 225-245 6-27 (192)
65 smart00235 ZnMc Zinc-dependent 47.8 9.2 0.0002 32.0 1.1 11 228-238 88-98 (140)
66 PLN03208 E3 ubiquitin-protein 47.5 19 0.0004 33.0 3.0 31 8-39 17-47 (193)
67 PF14247 DUF4344: Domain of un 47.4 26 0.00057 32.6 4.1 38 226-265 92-129 (220)
68 PF10235 Cript: Microtubule-as 47.3 12 0.00026 30.1 1.6 24 29-54 58-81 (90)
69 cd04267 ZnMc_ADAM_like Zinc-de 47.3 13 0.00027 33.0 2.0 24 214-238 122-145 (192)
70 KOG4739 Uncharacterized protei 46.3 14 0.0003 34.7 2.1 42 13-54 7-49 (233)
71 cd04268 ZnMc_MMP_like Zinc-dep 46.2 11 0.00023 32.3 1.3 14 225-238 93-106 (165)
72 cd06158 S2P-M50_like_1 Unchara 46.1 14 0.00031 33.0 2.1 18 225-242 8-25 (181)
73 COG5152 Uncharacterized conser 46.0 5.5 0.00012 36.6 -0.6 45 10-55 197-243 (259)
74 PF01863 DUF45: Protein of unk 45.8 12 0.00027 33.3 1.7 27 212-238 150-176 (205)
75 TIGR02411 leuko_A4_hydro leuko 45.7 15 0.00034 39.0 2.6 40 227-266 280-321 (601)
76 COG1645 Uncharacterized Zn-fin 45.6 13 0.00028 31.9 1.6 24 84-114 31-54 (131)
77 PRK04860 hypothetical protein; 45.5 15 0.00034 32.4 2.2 27 222-249 59-88 (160)
78 KOG1420 Ca2+-activated K+ chan 44.4 27 0.00059 37.1 4.0 6 311-316 50-55 (1103)
79 KOG2130 Phosphatidylserine-spe 43.9 23 0.0005 34.9 3.3 12 149-160 200-211 (407)
80 PF00413 Peptidase_M10: Matrix 43.6 13 0.00029 31.3 1.5 18 221-238 100-117 (154)
81 TIGR02289 M3_not_pepF oligoend 42.3 30 0.00064 36.2 4.1 45 224-268 335-389 (549)
82 PRK14559 putative protein seri 41.8 25 0.00055 37.8 3.5 22 83-113 29-50 (645)
83 cd00203 ZnMc Zinc-dependent me 41.6 19 0.00042 30.6 2.2 16 223-238 93-108 (167)
84 PF12674 Zn_ribbon_2: Putative 41.3 11 0.00023 29.6 0.5 29 11-39 2-35 (81)
85 COG2888 Predicted Zn-ribbon RN 41.3 9.9 0.00022 28.2 0.3 15 83-97 11-25 (61)
86 KOG0490 Transcription factor, 40.7 5.3 0.00011 36.2 -1.6 51 77-128 19-69 (235)
87 PF13688 Reprolysin_5: Metallo 40.6 15 0.00033 32.5 1.4 18 221-238 137-154 (196)
88 PF08219 TOM13: Outer membrane 40.6 19 0.00041 28.0 1.7 25 223-248 49-73 (77)
89 PRK00420 hypothetical protein; 40.5 20 0.00043 30.0 1.9 26 83-114 25-50 (112)
90 PRK14873 primosome assembly pr 40.4 23 0.00049 38.3 2.9 52 186-238 502-555 (665)
91 PF05299 Peptidase_M61: M61 gl 39.5 15 0.00033 31.0 1.2 41 226-266 4-57 (122)
92 PRK02870 heat shock protein Ht 39.4 24 0.00053 34.9 2.7 24 214-237 157-184 (336)
93 KOG3714 Meprin A metalloprotea 39.3 14 0.0003 37.4 1.1 11 228-238 161-171 (411)
94 PRK14714 DNA polymerase II lar 38.9 38 0.00082 39.1 4.3 14 230-243 906-919 (1337)
95 KOG3624 M13 family peptidase [ 38.8 14 0.0003 39.8 0.9 15 225-239 517-531 (687)
96 PRK04897 heat shock protein Ht 38.6 13 0.00028 35.9 0.7 19 220-238 131-149 (298)
97 KOG3931 Uncharacterized conser 38.4 17 0.00036 36.3 1.3 24 219-242 98-121 (484)
98 KOG2932 E3 ubiquitin ligase in 37.9 16 0.00034 35.8 1.1 44 11-54 92-135 (389)
99 cd06162 S2P-M50_PDZ_SREBP Ster 37.8 21 0.00045 34.5 1.9 17 225-241 134-150 (277)
100 COG1451 Predicted metal-depend 37.6 16 0.00035 34.0 1.1 27 212-238 161-187 (223)
101 PRK00420 hypothetical protein; 37.4 20 0.00043 30.0 1.5 23 11-37 25-47 (112)
102 PRK11827 hypothetical protein; 37.3 25 0.00054 26.2 1.8 15 137-151 36-50 (60)
103 PF13574 Reprolysin_2: Metallo 37.1 20 0.00042 31.7 1.5 13 226-238 111-123 (173)
104 cd06159 S2P-M50_PDZ_Arch Uncha 36.9 23 0.00049 33.8 2.0 28 217-245 110-138 (263)
105 cd06161 S2P-M50_SpoIVFB SpoIVF 36.8 26 0.00057 31.9 2.4 22 224-245 36-58 (208)
106 PF04298 Zn_peptidase_2: Putat 35.9 21 0.00046 33.3 1.6 29 219-247 82-110 (222)
107 cd04279 ZnMc_MMP_like_1 Zinc-d 35.7 19 0.00042 30.8 1.2 16 223-238 101-116 (156)
108 PRK00807 50S ribosomal protein 35.6 11 0.00023 27.2 -0.4 35 44-91 3-38 (52)
109 PF06689 zf-C4_ClpX: ClpX C4-t 35.3 34 0.00074 23.2 2.2 31 83-113 3-33 (41)
110 PRK03001 M48 family peptidase; 35.0 18 0.0004 34.5 1.1 18 221-238 119-136 (283)
111 cd06164 S2P-M50_SpoIVFB_CBS Sp 34.8 27 0.00059 32.4 2.2 22 224-245 51-73 (227)
112 PRK14015 pepN aminopeptidase N 34.7 37 0.00081 37.9 3.5 41 226-266 296-338 (875)
113 PRK03072 heat shock protein Ht 34.6 18 0.00038 34.8 0.9 20 219-238 120-139 (288)
114 PRK05457 heat shock protein Ht 34.5 19 0.0004 34.7 1.0 19 220-238 128-146 (284)
115 PHA03309 transcriptional regul 34.4 31 0.00066 38.3 2.7 15 141-155 1494-1508(2033)
116 PF01400 Astacin: Astacin (Pep 34.2 32 0.0007 30.9 2.5 17 222-238 75-91 (191)
117 PF10463 Peptidase_U49: Peptid 34.2 44 0.00096 30.8 3.4 48 221-268 96-144 (206)
118 PRK03982 heat shock protein Ht 34.2 20 0.00043 34.3 1.2 18 221-238 120-137 (288)
119 cd04281 ZnMc_BMP1_TLD Zinc-dep 34.1 21 0.00045 32.7 1.2 11 228-238 89-99 (200)
120 PF06037 DUF922: Bacterial pro 33.8 64 0.0014 28.4 4.2 30 213-242 57-102 (161)
121 cd05709 S2P-M50 Site-2 proteas 33.8 26 0.00056 30.7 1.8 21 225-245 7-28 (180)
122 PRK01345 heat shock protein Ht 33.6 31 0.00067 33.7 2.4 18 221-238 119-136 (317)
123 COG2191 Formylmethanofuran deh 33.3 19 0.00041 33.1 0.8 30 82-113 173-202 (206)
124 PF04228 Zn_peptidase: Putativ 32.9 29 0.00063 33.7 2.1 46 223-268 167-227 (292)
125 cd04327 ZnMc_MMP_like_3 Zinc-d 32.9 26 0.00056 31.5 1.6 14 225-238 91-104 (198)
126 COG4784 Putative Zn-dependent 32.3 21 0.00046 35.6 1.0 47 214-261 107-158 (479)
127 PRK01265 heat shock protein Ht 31.7 35 0.00075 33.6 2.4 24 214-237 124-151 (324)
128 PRK02391 heat shock protein Ht 31.7 21 0.00045 34.5 0.9 19 220-238 127-145 (296)
129 cd06459 M3B_Oligoendopeptidase 31.6 48 0.001 32.9 3.5 38 224-261 220-260 (427)
130 KOG0978 E3 ubiquitin ligase in 31.2 11 0.00023 40.8 -1.3 46 10-56 644-692 (698)
131 COG0501 HtpX Zn-dependent prot 31.1 25 0.00054 33.1 1.3 18 221-238 152-169 (302)
132 cd04282 ZnMc_meprin Zinc-depen 30.9 25 0.00054 33.0 1.2 12 227-238 121-132 (230)
133 KOG3658 Tumor necrosis factor- 30.8 18 0.0004 38.8 0.3 22 218-239 382-405 (764)
134 cd04272 ZnMc_salivary_gland_MP 30.6 33 0.00071 31.3 2.0 15 224-238 143-157 (220)
135 PF13583 Reprolysin_4: Metallo 30.4 26 0.00056 31.9 1.2 11 228-238 139-149 (206)
136 cd04269 ZnMc_adamalysin_II_lik 30.2 45 0.00098 29.5 2.7 16 223-238 128-143 (194)
137 cd06160 S2P-M50_like_2 Unchara 29.8 41 0.00088 30.3 2.4 24 224-247 39-63 (183)
138 PF13582 Reprolysin_3: Metallo 29.8 26 0.00056 28.4 1.0 12 227-238 108-119 (124)
139 COG2738 Predicted Zn-dependent 29.6 27 0.00059 32.1 1.2 28 218-245 84-111 (226)
140 cd04283 ZnMc_hatching_enzyme Z 29.6 28 0.00061 31.4 1.3 12 227-238 78-89 (182)
141 PF02069 Metallothio_Pro: Prok 29.4 29 0.00064 25.0 1.1 28 11-38 9-37 (52)
142 KOG1047 Bifunctional leukotrie 28.8 26 0.00056 37.0 1.0 13 227-239 289-301 (613)
143 TIGR02414 pepN_proteo aminopep 28.4 48 0.001 36.9 3.1 41 226-266 283-325 (863)
144 PRK09672 phage exclusion prote 28.2 69 0.0015 31.3 3.7 48 220-267 159-207 (305)
145 COG0308 PepN Aminopeptidase N 28.1 31 0.00067 38.3 1.5 38 229-268 310-351 (859)
146 KOG3314 Ku70-binding protein [ 28.0 34 0.00074 30.6 1.5 16 226-241 91-106 (194)
147 cd02249 ZZ Zinc finger, ZZ typ 27.4 34 0.00074 23.5 1.1 14 10-23 1-14 (46)
148 PF13834 DUF4193: Domain of un 27.4 21 0.00046 29.2 0.1 31 79-110 68-98 (99)
149 KOG2462 C2H2-type Zn-finger pr 27.4 38 0.00082 32.6 1.8 16 7-22 128-143 (279)
150 cd06461 M2_ACE Peptidase famil 27.1 58 0.0012 33.8 3.2 34 229-263 250-291 (477)
151 PF13248 zf-ribbon_3: zinc-rib 26.4 39 0.00084 20.5 1.1 21 83-112 4-24 (26)
152 TIGR00181 pepF oligoendopeptid 26.3 32 0.0007 36.1 1.2 16 223-238 375-390 (591)
153 PF13923 zf-C3HC4_2: Zinc fing 26.1 58 0.0012 21.2 2.0 36 84-121 1-36 (39)
154 smart00291 ZnF_ZZ Zinc-binding 25.4 41 0.00088 22.9 1.2 30 10-39 5-36 (44)
155 cd04278 ZnMc_MMP Zinc-dependen 25.0 34 0.00073 29.4 0.9 16 222-237 103-118 (157)
156 PF05572 Peptidase_M43: Pregna 25.0 39 0.00084 29.5 1.3 19 222-241 65-83 (154)
157 PRK11595 DNA utilization prote 24.8 46 0.00099 30.7 1.8 37 11-53 7-45 (227)
158 cd04280 ZnMc_astacin_like Zinc 24.7 36 0.00079 30.2 1.1 12 227-238 75-86 (180)
159 PF07607 DUF1570: Protein of u 24.3 85 0.0018 26.7 3.2 32 228-259 3-38 (128)
160 PF11928 DUF3446: Domain of un 24.1 85 0.0018 24.9 2.9 9 252-260 17-25 (84)
161 PHA02624 large T antigen; Prov 23.8 1.6E+02 0.0034 31.9 5.7 23 302-324 149-171 (647)
162 PF12156 ATPase-cat_bd: Putati 23.4 54 0.0012 25.9 1.7 10 44-53 2-11 (88)
163 COG2835 Uncharacterized conser 23.4 61 0.0013 24.1 1.9 40 82-149 9-48 (60)
164 PRK12495 hypothetical protein; 23.3 39 0.00085 31.5 1.0 25 8-37 41-65 (226)
165 cd06163 S2P-M50_PDZ_RseP-like 22.8 54 0.0012 29.5 1.8 21 225-245 8-29 (182)
166 KOG2661 Peptidase family M48 [ 22.6 55 0.0012 32.6 1.9 27 215-241 259-290 (424)
167 PF04570 DUF581: Protein of un 22.4 54 0.0012 24.2 1.4 30 84-113 19-49 (58)
168 smart00834 CxxC_CXXC_SSSS Puta 22.2 43 0.00093 21.8 0.8 11 10-20 6-16 (41)
169 COG3590 PepO Predicted metallo 21.8 23 0.0005 37.5 -0.8 16 226-241 487-502 (654)
170 PF09471 Peptidase_M64: IgA Pe 21.3 47 0.001 31.7 1.2 18 225-242 215-232 (264)
171 PF12725 DUF3810: Protein of u 21.2 50 0.0011 32.3 1.4 34 220-263 190-223 (318)
172 PF09723 Zn-ribbon_8: Zinc rib 21.2 47 0.001 22.5 0.8 12 10-21 6-17 (42)
173 KOG4443 Putative transcription 21.1 50 0.0011 35.5 1.4 17 315-331 483-499 (694)
174 KOG0823 Predicted E3 ubiquitin 21.0 84 0.0018 29.5 2.7 54 8-64 46-104 (230)
175 PF06827 zf-FPG_IleRS: Zinc fi 20.6 65 0.0014 19.9 1.3 12 43-54 2-13 (30)
176 cd06258 Peptidase_M3_like The 20.3 1.5E+02 0.0032 29.0 4.5 32 228-259 156-191 (365)
177 PF01432 Peptidase_M3: Peptida 20.2 1.6E+02 0.0035 29.8 4.9 16 226-241 242-257 (458)
178 cd02336 ZZ_RSC8 Zinc finger, Z 20.1 86 0.0019 21.8 2.0 30 83-113 2-32 (45)
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=1.8e-77 Score=536.27 Aligned_cols=194 Identities=78% Similarity=1.208 Sum_probs=182.6
Q ss_pred hccceeccccccchhcHHHHHHhhcCcCCCCCCCCCcCCccccccceecceecccccCCCcccccccccccccccceeEE
Q 019740 134 GLNMKVEQQVPLLLVERQALNEAMEGEKNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEVT 213 (336)
Q Consensus 134 glg~~i~~~~p~~lV~~~ALn~a~~~e~~g~~h~~~~rGl~~~E~~~~~s~~~~~r~~~~~~~~~~~t~~~~~~~~~~v~ 213 (336)
||||||++++||+||+++|||+|.++|++|++|.++|||||++|+|+++++.|+|++++++++++|+|+|++++|+|+||
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 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEecCCChhhhhhhHHHHHHHHHHHhcCCCCCCcchhhhHHHHHHHHhhhcccccCCCCCccCCCCCCCCCCCCCCCC
Q 019740 214 AILILYGLPRLLTGSILAHEMMHAWLRLKGYPNLRPDVEEGICQVLAHMWLESEIYSGSGSDVASSSSSSASSSSSSPSS 293 (336)
Q Consensus 214 ~ilvl~glp~~~~~~~lahe~~ha~l~~~g~~~l~~~veeg~cq~~a~~wl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 293 (336)
+|+|||||||++||||||||+|||||||+||++|+|+||||||||||||||+++++++++ +++++|+|++++
T Consensus 81 ~Ilvl~GLPrll~gsiLAHE~mHa~Lrl~g~~~L~~~vEEGiCqvla~~wL~~~~~~~~~--------~~~~~s~~~s~~ 152 (212)
T PF12315_consen 81 AILVLYGLPRLLTGSILAHELMHAWLRLNGFPNLSPEVEEGICQVLAYLWLESELASGSG--------SSSSSSSSSSSS 152 (212)
T ss_pred EEEEECCCCHHHHhhHHHHHHHHHHhcccCCCCCChHHHHHHHHHHHHHHHhhhhhcccC--------CcccccCCCCCC
Confidence 999999999999999999999999999999999999999999999999999999998765 111234455566
Q ss_pred CCCCCCCCCCchHHHHHHHHHhhhhhcCCCCCCchhhhhhhc
Q 019740 294 SSTSSKKGKRSDFEKDLGKFFKHQIESDTSSAYGDGLGKVVR 335 (336)
Q Consensus 294 ~~~~~~~~~~~~~~~~l~~~~~~~i~~d~s~~yg~gfr~~~~ 335 (336)
++++||||++++||+||++||+||||+|+|||||||||+|++
T Consensus 153 ~~~~skkg~~s~~E~kL~~f~~~qIe~D~SpvYGdGFRaa~~ 194 (212)
T PF12315_consen 153 ASSSSKKGAKSQFEKKLGEFFKHQIETDTSPVYGDGFRAANE 194 (212)
T ss_pred cccccccccccHHHHHHHHHHHHHhccCCCcccchHHHHHHH
Confidence 677889999999999999999999999999999999999985
No 2
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.91 E-value=7.5e-26 Score=207.08 Aligned_cols=153 Identities=27% Similarity=0.498 Sum_probs=127.2
Q ss_pred CCcccCCCeeecCCCCCCCCCceeecCCccccccccccccCCcCcccCCcccCCCCceEEEeeec---------------
Q 019740 2 EAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHP--------------- 66 (336)
Q Consensus 2 g~~wH~~CF~C~~C~~~L~~~~F~~~dg~~yC~~CY~~~~~pkC~~C~~~I~~~~~g~i~~~~~~--------------- 66 (336)
|..||.+||+|+.|-.|+.+..|++.+|+.||+.||+.+|+|.|..|+++|.+. +|.++..+
T Consensus 33 ge~wH~~CFvCAQCf~pf~~g~~~efEgRkYCEhDF~~LfaPcC~kC~EFiiGr---VikamnnSwHp~CF~Cd~Cn~~L 109 (332)
T KOG2272|consen 33 GELWHEQCFVCAQCFRPFPDGIFYEFEGRKYCEHDFHVLFAPCCGKCGEFIIGR---VIKAMNNSWHPACFRCDLCNKHL 109 (332)
T ss_pred chhhHHHHHHHHHhcCcCCCceeEEecCcccccccchhhhchhhcccccchhhH---HHHhhccccCcccchhHHHHHHH
Confidence 578999999999999999999999999999999999999999999999999874 33333222
Q ss_pred --------------------------------------------ccccccCCCCcCCCCCccCCCCccCCCCCceEEcCC
Q 019740 67 --------------------------------------------FWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDD 102 (336)
Q Consensus 67 --------------------------------------------fW~qkyCp~H~H~~CF~C~~C~~~l~~~~~f~~~~d 102 (336)
|-+..| |+..|+|..|++.|..+.+-+ .
T Consensus 110 ad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d~y-----H~yHFkCt~C~keL~sdaRev---k 181 (332)
T KOG2272|consen 110 ADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGDPY-----HPYHFKCTTCGKELTSDAREV---K 181 (332)
T ss_pred hhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccccccccCCCC-----Cccceecccccccccchhhhh---c
Confidence 111223 555588999999998776643 7
Q ss_pred CceeccchhhhcccCCCCCCchhhHHHHHHhhccceeccccccchhcHHHHHHhhc----------CcCCCCCCCCCcCC
Q 019740 103 GRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAME----------GEKNGHHHLPETRG 172 (336)
Q Consensus 103 G~~yC~~C~~~~v~~~~~C~~c~~~I~~f~~glg~~i~~~~p~~lV~~~ALn~a~~----------~e~~g~~h~~~~rG 172 (336)
|.+||+.|+++ |..++|.+|.+||.+ ++ +.|||++|+ +||.||.|| |++|
T Consensus 182 ~eLyClrChD~--mgipiCgaC~rpIee-----------rv------i~amgKhWHveHFvCa~CekPFlGHrHY-EkkG 241 (332)
T KOG2272|consen 182 GELYCLRCHDK--MGIPICGACRRPIEE-----------RV------IFAMGKHWHVEHFVCAKCEKPFLGHRHY-EKKG 241 (332)
T ss_pred cceeccccccc--cCCcccccccCchHH-----------HH------HHHhccccchhheeehhcCCcccchhhh-hhcC
Confidence 89999999999 899999999988863 43 789999995 468999998 9999
Q ss_pred ccccccceeccee
Q 019740 173 LCLSEEQTVTTVL 185 (336)
Q Consensus 173 l~~~E~~~~~s~~ 185 (336)
|+|||+||+..+.
T Consensus 242 laYCe~h~~qLfG 254 (332)
T KOG2272|consen 242 LAYCETHYHQLFG 254 (332)
T ss_pred chhHHHHHHHHhh
Confidence 9999999986654
No 3
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.89 E-value=8.5e-24 Score=214.90 Aligned_cols=302 Identities=43% Similarity=0.675 Sum_probs=247.4
Q ss_pred CeeecCCCCCCCCCceeecCCcccccccccc-ccCCcCcccCCcccCCCCceEEEeeecccccccCCCCcCCCCCccCCC
Q 019740 9 CFRCHSCNLPITDVEFSMSGNRPYHKHCYKE-QHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSC 87 (336)
Q Consensus 9 CF~C~~C~~~L~~~~F~~~dg~~yC~~CY~~-~~~pkC~~C~~~I~~~~~g~i~~~~~~fW~qkyCp~H~H~~CF~C~~C 87 (336)
||.|..|..++ ..+...+|.. ...+.+.++...|.....+.+.++...+|.|+||+.|.+.....|..|
T Consensus 151 ~~~~~~~~~p~----------~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~tp~~~~~ 220 (479)
T KOG1703|consen 151 CFQCKRCSEPL----------SGFPKPSYHESGRSKNEDVEEASSPSSRAGLILSRSHPFWKQKYCPSHENDGTPKCCSC 220 (479)
T ss_pred hhhhccccccc----------CCccccccccccccccccccccccccccccccccccchhhhhcccccccCCCCCCcccc
Confidence 55666666665 2334455554 366789999999987766778889999999999999999999999999
Q ss_pred CccCCCCCceEEcCCCceeccchhhhcccCCCCCCchhhHHHHHHhhccceeccccccchhcHHHHHHhhcCcCCCCCCC
Q 019740 88 ERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEKNGHHHL 167 (336)
Q Consensus 88 ~~~l~~~~~f~~~~dG~~yC~~C~~~~v~~~~~C~~c~~~I~~f~~glg~~i~~~~p~~lV~~~ALn~a~~~e~~g~~h~ 167 (336)
.+..+.+..+..+.+++.+|.+|....+++.+++++....+..++.+..+++++..+++++...+++++-...+....|.
T Consensus 221 ~r~e~~~~~~~~l~~~~~~~~~~~~~~~~~~p~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 300 (479)
T KOG1703|consen 221 ERLEPLDTRYVELADGRALCLECMGSASMDSPECQPLVSAPRPASEGLHMKVEKELPLLLVESEALKKLREEEKPAEYHN 300 (479)
T ss_pred cccccccccceecccchhhhhhccCCcccCCCccCcceecccccccccccccccccchhhcccccccccccccccccccc
Confidence 99886688888998889999999987789999999999999999999999999999999999999999988777665554
Q ss_pred CCcCCccccccceecceecccccCCCcccccccccccccccceeEEEEEEecCCChhhhhhhHHHHHHHHHHHhcCCCCC
Q 019740 168 PETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEVTAILILYGLPRLLTGSILAHEMMHAWLRLKGYPNL 247 (336)
Q Consensus 168 ~~~rGl~~~E~~~~~s~~~~~r~~~~~~~~~~~t~~~~~~~~~~v~~ilvl~glp~~~~~~~lahe~~ha~l~~~g~~~l 247 (336)
.++++|..+.++++++ ..+.++.++..+....|++++|+++++.|+...|.+++||+||+|++.++++.+
T Consensus 301 -~~~p~c~~c~~~i~~~---------~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~ 370 (479)
T KOG1703|consen 301 -VTRPLCLSCNQKIRSV---------KVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCL 370 (479)
T ss_pred -cccccccccccCcccc---------eeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccC
Confidence 8899999999998553 345678888888889999999999999999999999999999999999999999
Q ss_pred CcchhhhHHHHHHHHhhhcccccCCC-CCccCCCCCCCCCCCCCCCCCCCCCCCCC--CchHHHHHHHHHhhhhhcCCCC
Q 019740 248 RPDVEEGICQVLAHMWLESEIYSGSG-SDVASSSSSSASSSSSSPSSSSTSSKKGK--RSDFEKDLGKFFKHQIESDTSS 324 (336)
Q Consensus 248 ~~~veeg~cq~~a~~wl~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~i~~d~s~ 324 (336)
.+.+||+||++ +.+|++..-+-..- ..... .+....+..+......++.. +..++++.++|+.++|+.|.++
T Consensus 371 ~~i~~~~v~a~-~~~wH~~cf~C~~C~~~~~~----~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~~~~~ie~~~~~ 445 (479)
T KOG1703|consen 371 LPILEEGVCAL-GRLWHPECFVCADCGKPLKN----SSFFESDGEPYCEDHYKKLFTTKCDYCKKPVEFGSRQIEADGSP 445 (479)
T ss_pred CchHHhHhhhc-cCeechhceeeecccCCCCC----CcccccCCccchhhhHhhhccccchhccchhHhhhhHhhccCcc
Confidence 99999999999 99999998765422 11110 00111222222233334443 7788999999999999999999
Q ss_pred CCchhhhhhhc
Q 019740 325 AYGDGLGKVVR 335 (336)
Q Consensus 325 ~yg~gfr~~~~ 335 (336)
.||||||.++.
T Consensus 446 ~h~~~F~c~~c 456 (479)
T KOG1703|consen 446 FHGDCFRCANC 456 (479)
T ss_pred ccccceehhhh
Confidence 99999998864
No 4
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.82 E-value=1.9e-22 Score=196.19 Aligned_cols=145 Identities=20% Similarity=0.407 Sum_probs=124.5
Q ss_pred CCCcccCCCeeecCCCCCCCCCceeecCCccccccccccccCCcCcccCCcccCCCCceEEEeeecccccccCCCCcCCC
Q 019740 1 MEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDG 80 (336)
Q Consensus 1 lg~~wH~~CF~C~~C~~~L~~~~F~~~dg~~yC~~CY~~~~~pkC~~C~~~I~~~~~g~i~~~~~~fW~qkyCp~H~H~~ 80 (336)
|++.||.+||+|..|++.|.++.||..|+++||+.||.+ ...||.+|+++|.+. ++.+.++.| |++
T Consensus 294 m~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~-tlekC~~Cg~~I~d~---iLrA~Gkay----------Hp~ 359 (468)
T KOG1701|consen 294 MDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQD-TLEKCNKCGEPIMDR---ILRALGKAY----------HPG 359 (468)
T ss_pred hhhhhcccceehHhhhhhhccccccccCCcccchHHHHH-HHHHHhhhhhHHHHH---HHHhccccc----------CCC
Confidence 789999999999999999999999999999999999986 678999999999975 789999998 999
Q ss_pred CCccCCCCccCCCCCceEEcCCCceeccchhhhcccCCCCCCchhhHHHHHHhhccceeccccccchhcHHHHHHhhcCc
Q 019740 81 TPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGE 160 (336)
Q Consensus 81 CF~C~~C~~~l~~~~~f~~~~dG~~yC~~C~~~~v~~~~~C~~c~~~I~~f~~glg~~i~~~~p~~lV~~~ALn~a~~~e 160 (336)
||+|..|.+.|. |..|....++++||..||.+ .++++|..|.+||+ |-+++- ..|.+.||++.+|.+
T Consensus 360 CF~Cv~C~r~ld-gipFtvd~~n~v~Cv~dfh~--kfAPrCs~C~~PI~--------P~~G~~--etvRvvamdr~fHv~ 426 (468)
T KOG1701|consen 360 CFTCVVCARCLD-GIPFTVDSQNNVYCVPDFHK--KFAPRCSVCGNPIL--------PRDGKD--ETVRVVAMDRDFHVN 426 (468)
T ss_pred ceEEEEeccccC-CccccccCCCceeeehhhhh--hcCcchhhccCCcc--------CCCCCc--ceEEEEEcccccccc
Confidence 999999999996 89998888999999999999 89999999999994 554332 235677888888765
Q ss_pred CCCCCCCCCcCCcccc
Q 019740 161 KNGHHHLPETRGLCLS 176 (336)
Q Consensus 161 ~~g~~h~~~~rGl~~~ 176 (336)
.-. -|--|+-|+
T Consensus 427 CY~----CEDCg~~LS 438 (468)
T KOG1701|consen 427 CYK----CEDCGLLLS 438 (468)
T ss_pred cee----hhhcCcccc
Confidence 421 155566666
No 5
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.72 E-value=3.5e-18 Score=166.67 Aligned_cols=103 Identities=24% Similarity=0.527 Sum_probs=91.0
Q ss_pred CCCcccCCCeeecCCCCCCCCCceee-cCCccccccccccccCCcCcccCCcccCCCCc----eEEEeeecccccccCCC
Q 019740 1 MEAFWHPECFRCHSCNLPITDVEFSM-SGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAG----LIEYRAHPFWLQKYCPS 75 (336)
Q Consensus 1 lg~~wH~~CF~C~~C~~~L~~~~F~~-~dg~~yC~~CY~~~~~pkC~~C~~~I~~~~~g----~i~~~~~~fW~qkyCp~ 75 (336)
||+.||+.||+|..|++.|++..|.+ .++++||.+||+++|+|+|++|+++|...++. .|.++++.|
T Consensus 352 ~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etvRvvamdr~f-------- 423 (468)
T KOG1701|consen 352 LGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETVRVVAMDRDF-------- 423 (468)
T ss_pred cccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCCcceEEEEEccccc--------
Confidence 68999999999999999999999986 78999999999999999999999999986542 245666666
Q ss_pred CcCCCCCccCCCCccCC---CCCceEEcCCCceeccchhhhc
Q 019740 76 HERDGTPRCCSCERMEP---RDTKYLSLDDGRKLCLECLDSA 114 (336)
Q Consensus 76 H~H~~CF~C~~C~~~l~---~~~~f~~~~dG~~yC~~C~~~~ 114 (336)
|.+|++|..|+..|. .+...|.+ ||.++|+.|+.+.
T Consensus 424 --Hv~CY~CEDCg~~LS~e~e~qgCyPl-d~HllCk~Ch~~R 462 (468)
T KOG1701|consen 424 --HVNCYKCEDCGLLLSSEEEGQGCYPL-DGHLLCKTCHLKR 462 (468)
T ss_pred --cccceehhhcCccccccCCCCcceec-cCceeechhhhhh
Confidence 999999999999986 36678899 9999999998764
No 6
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.59 E-value=4.8e-17 Score=151.76 Aligned_cols=101 Identities=22% Similarity=0.564 Sum_probs=89.8
Q ss_pred CCCcccCCCeeecCCCCCCCCCceeecCCccccccccccccCCcCcccCCcccCCCCceE-EEeeecccccccCCCCcCC
Q 019740 1 MEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLI-EYRAHPFWLQKYCPSHERD 79 (336)
Q Consensus 1 lg~~wH~~CF~C~~C~~~L~~~~F~~~dg~~yC~~CY~~~~~pkC~~C~~~I~~~~~g~i-~~~~~~fW~qkyCp~H~H~ 79 (336)
|++.||..|++|+.|+.+|++..| .++|.+||+++|.++|+.||..|...|++. ++| .+.+..| |.
T Consensus 52 l~R~wHs~CLkCs~C~~qL~drCF-sR~~s~yCkedFfKrfGTKCsaC~~GIpPt--qVVRkAqd~VY----------Hl 118 (383)
T KOG4577|consen 52 LDRHWHSSCLKCSDCHDQLADRCF-SREGSVYCKEDFFKRFGTKCSACQEGIPPT--QVVRKAQDFVY----------HL 118 (383)
T ss_pred HhhhhhhhhcchhhhhhHHHHHHh-hcCCceeehHHHHHHhCCcchhhcCCCChH--HHHHHhhccee----------eh
Confidence 578999999999999999998655 589999999999999999999999999985 233 3445555 99
Q ss_pred CCCccCCCCccCCCCCceEEcCCCceeccchhhhc
Q 019740 80 GTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSA 114 (336)
Q Consensus 80 ~CF~C~~C~~~l~~~~~f~~~~dG~~yC~~C~~~~ 114 (336)
.||.|..|.+.|..|+.||..+|+++.|++.|+++
T Consensus 119 ~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~A 153 (383)
T KOG4577|consen 119 HCFACFICKRQLATGDEFYLMEDARLVCKDDYETA 153 (383)
T ss_pred hhhhhHhhhcccccCCeeEEeccceeehhhhHHHH
Confidence 99999999999999999999999999999999985
No 7
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.54 E-value=1.8e-15 Score=152.19 Aligned_cols=192 Identities=15% Similarity=0.260 Sum_probs=148.0
Q ss_pred CCcccCCCeeecCCCCCCCCCceeecCCccccccccccccCCcCcccCCcccCCCCceEEEeeecccccccCCCCcCCCC
Q 019740 2 EAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGT 81 (336)
Q Consensus 2 g~~wH~~CF~C~~C~~~L~~~~F~~~dg~~yC~~CY~~~~~pkC~~C~~~I~~~~~g~i~~~~~~fW~qkyCp~H~H~~C 81 (336)
++.||..||.|..|++.|+...|+.+++. +++++ ..|.+.|.++ +|.+.++.| |+.|
T Consensus 35 d~~fhi~cf~c~~cg~~la~~gff~k~~~--------~~ygt--~~c~~~~~ge---vvsa~gkty----------h~~c 91 (670)
T KOG1044|consen 35 DNHFHINCFQCKKCGRNLAEGGFFTKPEN--------RLYGT--DDCRAFVEGE---VVSTLGKTY----------HPKC 91 (670)
T ss_pred ccccceeeeeccccCCCcccccceecccc--------eeecc--cchhhhccce---eEeccccee----------cccc
Confidence 67899999999999999999999998775 45555 7899999986 789999988 9999
Q ss_pred CccCCCCccCCCCCceEEcCCCceeccchhhhccc------CCCCCCchhhHHHHHHhhccceeccccccchhcHHHHHH
Q 019740 82 PRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIM------DTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNE 155 (336)
Q Consensus 82 F~C~~C~~~l~~~~~f~~~~dG~~yC~~C~~~~v~------~~~~C~~c~~~I~~f~~glg~~i~~~~p~~lV~~~ALn~ 155 (336)
|.|+.|..+++.|++- ........|..|...+-. +...|.+|...|.. ++. +-||++
T Consensus 92 f~cs~ck~pf~~g~~v-t~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~----------gq~------llald~ 154 (670)
T KOG1044|consen 92 FSCSTCKSPFKSGDKV-TFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKN----------GQA------LLALDK 154 (670)
T ss_pred ceecccCCCCCCCCee-eecchhhhhhhhcCcccCCcccccCCccccchhhhhhc----------cce------eeeecc
Confidence 9999999999987774 554666889999766522 45679999887752 343 338888
Q ss_pred hhcCc--------CCCCCCCCCcCCccccccceecceecccccCCC-----ccccccccccccccc-ceeEEEEEEecCC
Q 019740 156 AMEGE--------KNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAG-----YRLIDMITEPYRLIR-RCEVTAILILYGL 221 (336)
Q Consensus 156 a~~~e--------~~g~~h~~~~rGl~~~E~~~~~s~~~~~r~~~~-----~~~~~~~t~~~~~~~-~~~v~~ilvl~gl 221 (336)
+||.- ...++.|+.++|++|||.+|+.-+. .+.-.. .++++.....++.+. ||....-+.--|-
T Consensus 155 qwhv~cfkc~~c~~vL~gey~skdg~pyce~dy~~~fg--vkc~~c~~fisgkvLqag~kh~HPtCARCsRCgqmF~eGE 232 (670)
T KOG1044|consen 155 QWHVSCFKCKSCSAVLNGEYMSKDGVPYCEKDYQAKFG--VKCEECEKFISGKVLQAGDKHFHPTCARCSRCGQMFGEGE 232 (670)
T ss_pred ceeeeeeehhhhcccccceeeccCCCcchhhhhhhhcC--eehHHhhhhhhhhhhhccCcccCcchhhhhhhccccccch
Confidence 88642 3445668899999999999986654 111111 223455556677776 7888899999999
Q ss_pred ChhhhhhhHHHHHH
Q 019740 222 PRLLTGSILAHEMM 235 (336)
Q Consensus 222 p~~~~~~~lahe~~ 235 (336)
-+.|.||.+||.-.
T Consensus 233 EMYlQGs~iWHP~C 246 (670)
T KOG1044|consen 233 EMYLQGSEIWHPDC 246 (670)
T ss_pred heeeccccccCCcc
Confidence 99999999999754
No 8
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.53 E-value=3.3e-15 Score=152.24 Aligned_cols=153 Identities=16% Similarity=0.272 Sum_probs=119.4
Q ss_pred CCCcccCCCeeecCCCCCCCCCceeecCCccccccccccccCCcCcccCCcccCCCCceEEEeeecccccccCCCCcCCC
Q 019740 1 MEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDG 80 (336)
Q Consensus 1 lg~~wH~~CF~C~~C~~~L~~~~F~~~dg~~yC~~CY~~~~~pkC~~C~~~I~~~~~g~i~~~~~~fW~qkyCp~H~H~~ 80 (336)
||+.||+.+|.|..|...|....|...+|++||..||.+.+.|+|..|.++|.++ .|.+.++. ||+.
T Consensus 322 ~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~---~v~a~~~~----------wH~~ 388 (479)
T KOG1703|consen 322 LGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEE---GVCALGRL----------WHPE 388 (479)
T ss_pred ccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHh---HhhhccCe----------echh
Confidence 6889999999999999999998998999999999999999999999999999987 46666543 4999
Q ss_pred CCccCCCCccCCCCCceEEcCCCceeccchhhhcccCCCCCCchhhHHHH---HHhhccceeccccccchhcHHHHHHhh
Q 019740 81 TPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQE---FYEGLNMKVEQQVPLLLVERQALNEAM 157 (336)
Q Consensus 81 CF~C~~C~~~l~~~~~f~~~~dG~~yC~~C~~~~v~~~~~C~~c~~~I~~---f~~glg~~i~~~~p~~lV~~~ALn~a~ 157 (336)
||.|..|++.+. +..|+.. ||.+||..|+.. .+...|..|.+||.. +.+++|.++.+..- .....++++
T Consensus 389 cf~C~~C~~~~~-~~~~~~~-~~~pyce~~~~~--~~~~~~~~~~~p~~~~~~~ie~~~~~~h~~~F----~c~~c~~~l 460 (479)
T KOG1703|consen 389 CFVCADCGKPLK-NSSFFES-DGEPYCEDHYKK--LFTTKCDYCKKPVEFGSRQIEADGSPFHGDCF----RCANCMKKL 460 (479)
T ss_pred ceeeecccCCCC-CCccccc-CCccchhhhHhh--hccccchhccchhHhhhhHhhccCccccccce----ehhhhhccc
Confidence 999999999996 6666655 999999999998 566789889888763 44556666654431 122222222
Q ss_pred cCcCCCCCCCCCcCCccccccc
Q 019740 158 EGEKNGHHHLPETRGLCLSEEQ 179 (336)
Q Consensus 158 ~~e~~g~~h~~~~rGl~~~E~~ 179 (336)
..+-+.++.+.+||..+
T Consensus 461 -----~~~~~~~~~~~p~c~~~ 477 (479)
T KOG1703|consen 461 -----TKKTFFETLDKPLCQKH 477 (479)
T ss_pred -----cCCceeecCCccccccC
Confidence 22235678888888654
No 9
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.50 E-value=1.8e-15 Score=139.18 Aligned_cols=99 Identities=20% Similarity=0.507 Sum_probs=92.5
Q ss_pred CCCcccCCCeeecCCCCCCCCCceeecCCccccccccccccCCcCcccCCcccCCCCceEEEeeecccccccCCCCcCCC
Q 019740 1 MEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDG 80 (336)
Q Consensus 1 lg~~wH~~CF~C~~C~~~L~~~~F~~~dg~~yC~~CY~~~~~pkC~~C~~~I~~~~~g~i~~~~~~fW~qkyCp~H~H~~ 80 (336)
||+.||.++|+|+.|.+|+-+...|++.|.+||+++|.++|+..|..|+..|.+. ++.+.++.| -+.
T Consensus 213 mgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~---vv~al~Kaw----------Cv~ 279 (332)
T KOG2272|consen 213 MGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGGD---VVSALNKAW----------CVE 279 (332)
T ss_pred hccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhheecCCccCcc---HHHHhhhhh----------ccc
Confidence 7999999999999999999999999999999999999999999999999999985 788888884 677
Q ss_pred CCccCCCCccCCCCCceEEcCCCceeccchhhh
Q 019740 81 TPRCCSCERMEPRDTKYLSLDDGRKLCLECLDS 113 (336)
Q Consensus 81 CF~C~~C~~~l~~~~~f~~~~dG~~yC~~C~~~ 113 (336)
||.|+.|++.|....+|+++ |-+|.|+.||++
T Consensus 280 cf~Cs~Cdkkl~~K~Kf~E~-DmkP~CKkCy~r 311 (332)
T KOG2272|consen 280 CFSCSTCDKKLTQKNKFYEF-DMKPVCKKCYDR 311 (332)
T ss_pred cccccccccccccccceeee-ccchHHHHHHhh
Confidence 79999999999988899999 899999999986
No 10
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.40 E-value=5.5e-14 Score=141.62 Aligned_cols=97 Identities=23% Similarity=0.602 Sum_probs=85.7
Q ss_pred CCCcccCCCeeecCCCCCCCCCceeecCCccccccccccccCCcCcccCCcccCCCCceEEEeeecccccccCCCCcCCC
Q 019740 1 MEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDG 80 (336)
Q Consensus 1 lg~~wH~~CF~C~~C~~~L~~~~F~~~dg~~yC~~CY~~~~~pkC~~C~~~I~~~~~g~i~~~~~~fW~qkyCp~H~H~~ 80 (336)
|++.||..||+|..|...|.+ +|..+||.|||..||++.|+.+|..|.++|.+. ++.+.++.| |+.
T Consensus 152 ld~qwhv~cfkc~~c~~vL~g-ey~skdg~pyce~dy~~~fgvkc~~c~~fisgk---vLqag~kh~----------HPt 217 (670)
T KOG1044|consen 152 LDKQWHVSCFKCKSCSAVLNG-EYMSKDGVPYCEKDYQAKFGVKCEECEKFISGK---VLQAGDKHF----------HPT 217 (670)
T ss_pred eccceeeeeeehhhhcccccc-eeeccCCCcchhhhhhhhcCeehHHhhhhhhhh---hhhccCccc----------Ccc
Confidence 689999999999999999976 899999999999999999999999999999985 788888644 999
Q ss_pred CCccCCCCccCCCCCceEEcCCCceeccchhh
Q 019740 81 TPRCCSCERMEPRDTKYLSLDDGRKLCLECLD 112 (336)
Q Consensus 81 CF~C~~C~~~l~~~~~f~~~~dG~~yC~~C~~ 112 (336)
|-+|..|+.+|..|+..|.. ...++-..|-.
T Consensus 218 CARCsRCgqmF~eGEEMYlQ-Gs~iWHP~C~q 248 (670)
T KOG1044|consen 218 CARCSRCGQMFGEGEEMYLQ-GSEIWHPDCKQ 248 (670)
T ss_pred hhhhhhhccccccchheeec-cccccCCcccc
Confidence 99999999999877776644 67777777764
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=98.87 E-value=5.2e-10 Score=81.21 Aligned_cols=41 Identities=44% Similarity=1.189 Sum_probs=38.1
Q ss_pred CCCcccCCCeeecCCCCCCCCCceeecCCcccccccccccc
Q 019740 1 MEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQH 41 (336)
Q Consensus 1 lg~~wH~~CF~C~~C~~~L~~~~F~~~dg~~yC~~CY~~~~ 41 (336)
+|+.||++||+|..|+++|.+..|+..+|++||+.||.++|
T Consensus 18 ~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 18 MGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp TTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred CCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 47899999999999999999988999999999999998765
No 12
>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=98.75 E-value=9.8e-09 Score=74.48 Aligned_cols=56 Identities=20% Similarity=0.468 Sum_probs=45.7
Q ss_pred CcccCCcccCCCCceEEEeeecccccccCCCCcCCCCCccCCCCccCCCCCceEEcCCCceeccchhhh
Q 019740 45 CDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDS 113 (336)
Q Consensus 45 C~~C~~~I~~~~~g~i~~~~~~fW~qkyCp~H~H~~CF~C~~C~~~l~~~~~f~~~~dG~~yC~~C~~~ 113 (336)
|..|+++|.+.. .++.+.++.| |+.||+|..|+++|. +..|+.. ||++||..|+.+
T Consensus 1 C~~C~~~I~~~~-~~~~~~~~~~----------H~~Cf~C~~C~~~l~-~~~~~~~-~~~~~C~~c~~~ 56 (58)
T PF00412_consen 1 CARCGKPIYGTE-IVIKAMGKFW----------HPECFKCSKCGKPLN-DGDFYEK-DGKPYCKDCYQK 56 (58)
T ss_dssp BTTTSSBESSSS-EEEEETTEEE----------ETTTSBETTTTCBTT-TSSEEEE-TTEEEEHHHHHH
T ss_pred CCCCCCCccCcE-EEEEeCCcEE----------EccccccCCCCCccC-CCeeEeE-CCEEECHHHHhh
Confidence 789999999864 2335777764 999999999999997 4447666 899999999976
No 13
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=98.47 E-value=3.3e-08 Score=90.24 Aligned_cols=98 Identities=27% Similarity=0.554 Sum_probs=76.5
Q ss_pred CCcccCCCeeecCCCCCCCCCceeecCCccccccccccccCC--------------------------------------
Q 019740 2 EAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHP-------------------------------------- 43 (336)
Q Consensus 2 g~~wH~~CF~C~~C~~~L~~~~F~~~dg~~yC~~CY~~~~~p-------------------------------------- 43 (336)
|..||+.||+|..|.+.|....+..+++.+||+.||...++|
T Consensus 27 g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g 106 (200)
T KOG1700|consen 27 GVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGKDGKSLNESKPNQSAKFQVFAG 106 (200)
T ss_pred CcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCCcccccccccccccchhHHhhhc
Confidence 678999999999999999998999999999999987554332
Q ss_pred ---cCcccCCcccCCCCceEEEeeecccccccCCCCcCCCCCccCCCCccCCCCCceEEcCCCceeccchhhh
Q 019740 44 ---KCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDS 113 (336)
Q Consensus 44 ---kC~~C~~~I~~~~~g~i~~~~~~fW~qkyCp~H~H~~CF~C~~C~~~l~~~~~f~~~~dG~~yC~~C~~~ 113 (336)
.|..|++.+.+.+ .+...+..| |..||+|..|+..|. ...|... +|.+||...+..
T Consensus 107 ~~~~c~~c~k~vy~~E--k~~~~~~~~----------hk~cfrc~~~~~~ls-~~~~~~~-~g~l~~~~~~~~ 165 (200)
T KOG1700|consen 107 EKEKCARCQKTVYPLE--KVTGNGLEF----------HKSCFRCTHCGKKLS-PKNYAAL-EGVLYCKHHFAQ 165 (200)
T ss_pred cccccccccceeeehH--HHhhhhhhh----------hhhheeecccccccC-Ccchhhc-CCccccchhhhe
Confidence 3888888776542 344555554 999999999999996 5566554 778888665544
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=97.54 E-value=6.4e-05 Score=49.37 Aligned_cols=38 Identities=16% Similarity=0.318 Sum_probs=30.2
Q ss_pred cCcccCCcccCCCCceEEEeeecccccccCCCCcCCCCCccCCCCccCC
Q 019740 44 KCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEP 92 (336)
Q Consensus 44 kC~~C~~~I~~~~~g~i~~~~~~fW~qkyCp~H~H~~CF~C~~C~~~l~ 92 (336)
+|..|+++|.+.. ..+.+.+..| |..||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~-~~~~~~~~~~----------H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGE-LVLRALGKVW----------HPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCc-EEEEeCCccc----------cccCCCCcccCCcCc
Confidence 5899999998852 3566666653 999999999999884
No 15
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=97.52 E-value=2.8e-06 Score=80.30 Aligned_cols=76 Identities=17% Similarity=0.324 Sum_probs=59.5
Q ss_pred ccccccCCcCcccCCcccCCCCceEEEeeecccccccCCCCcCCCCCccCCCCccCCCCCceEEcCCCceeccchhhhcc
Q 019740 36 CYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAI 115 (336)
Q Consensus 36 CY~~~~~pkC~~C~~~I~~~~~g~i~~~~~~fW~qkyCp~H~H~~CF~C~~C~~~l~~~~~f~~~~dG~~yC~~C~~~~v 115 (336)
++...--|+|+.|.+.|.+.- ++.+.+. |||..|.+|..|+.+| +++.+.. +|..||++.|-+
T Consensus 27 df~~~eip~CagC~q~IlDrF--ilKvl~R----------~wHs~CLkCs~C~~qL--~drCFsR-~~s~yCkedFfK-- 89 (383)
T KOG4577|consen 27 DFSNVEIPICAGCDQHILDRF--ILKVLDR----------HWHSSCLKCSDCHDQL--ADRCFSR-EGSVYCKEDFFK-- 89 (383)
T ss_pred cccccccccccchHHHHHHHH--HHHHHhh----------hhhhhhcchhhhhhHH--HHHHhhc-CCceeehHHHHH--
Confidence 344445789999999999863 3334443 6699999999999999 5666665 899999999998
Q ss_pred cCCCCCCchhhHH
Q 019740 116 MDTHECQPLYLEI 128 (336)
Q Consensus 116 ~~~~~C~~c~~~I 128 (336)
.+..+|.+|..-|
T Consensus 90 rfGTKCsaC~~GI 102 (383)
T KOG4577|consen 90 RFGTKCSACQEGI 102 (383)
T ss_pred HhCCcchhhcCCC
Confidence 6788899887655
No 16
>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=96.95 E-value=0.00035 Score=45.80 Aligned_cols=20 Identities=45% Similarity=1.411 Sum_probs=18.2
Q ss_pred CCCcccCCCeeecCCCCCCC
Q 019740 1 MEAFWHPECFRCHSCNLPIT 20 (336)
Q Consensus 1 lg~~wH~~CF~C~~C~~~L~ 20 (336)
+++.||++||+|..|+++|.
T Consensus 19 ~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 19 LGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CCccccccCCCCcccCCcCc
Confidence 47899999999999999985
No 17
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=96.48 E-value=0.00032 Score=64.13 Aligned_cols=99 Identities=19% Similarity=0.387 Sum_probs=73.5
Q ss_pred CCcccCCCeeecCCCCCCC--CCceeecCCcccccccccc--ccCCcCcccCCcccCCCCceEEEeeecccccccCCCCc
Q 019740 2 EAFWHPECFRCHSCNLPIT--DVEFSMSGNRPYHKHCYKE--QHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHE 77 (336)
Q Consensus 2 g~~wH~~CF~C~~C~~~L~--~~~F~~~dg~~yC~~CY~~--~~~pkC~~C~~~I~~~~~g~i~~~~~~fW~qkyCp~H~ 77 (336)
+..||..|..|..|..++. ...|.. +|..||..+|.. .+..+|..|...|...+ .....| ++.
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~-----~ler~f--~~~----- 82 (235)
T KOG0490|consen 16 DRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTISQLD-----ELERAF--EKV----- 82 (235)
T ss_pred cHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCcCHHH-----HHHHhh--cCC-----
Confidence 4679999999999999998 666666 999999999998 88899999999985432 222222 111
Q ss_pred CCCCCccCCCCccCCCCCceEEcCCCceeccchhhh
Q 019740 78 RDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDS 113 (336)
Q Consensus 78 H~~CF~C~~C~~~l~~~~~f~~~~dG~~yC~~C~~~ 113 (336)
|-.||.|..|...+..+..+......+.+|...+..
T Consensus 83 h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~ 118 (235)
T KOG0490|consen 83 HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKE 118 (235)
T ss_pred CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhh
Confidence 778999999998876566665443446666666544
No 18
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=95.65 E-value=0.022 Score=46.06 Aligned_cols=43 Identities=23% Similarity=0.280 Sum_probs=34.2
Q ss_pred CCChhhhhhhHHHHHHHHHHHhcC--CCCCCcchhhhHHHHHHHH
Q 019740 220 GLPRLLTGSILAHEMMHAWLRLKG--YPNLRPDVEEGICQVLAHM 262 (336)
Q Consensus 220 glp~~~~~~~lahe~~ha~l~~~g--~~~l~~~veeg~cq~~a~~ 262 (336)
+-+.-....+|+||+.|+|+.... ...++..+.||+++.++..
T Consensus 19 ~~~~~~~~~~l~HE~~H~~~~~~~~~~~~~~~W~~EG~A~y~~~~ 63 (128)
T PF13485_consen 19 GSDEDWLDRVLAHELAHQWFGNYFGGDDNAPRWFNEGLAEYVEGR 63 (128)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHcCCCccCchHHHHHHHHHHhcC
Confidence 444444459999999999988752 3588899999999999965
No 19
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=94.66 E-value=0.0068 Score=55.32 Aligned_cols=40 Identities=25% Similarity=0.832 Sum_probs=35.3
Q ss_pred CCCcccCCCeeecCCCCCCCCCceeecCCccccccccccc
Q 019740 1 MEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQ 40 (336)
Q Consensus 1 lg~~wH~~CF~C~~C~~~L~~~~F~~~dg~~yC~~CY~~~ 40 (336)
|++.||..||+|..|+.+|.-..+--.|.+|||...|.+.
T Consensus 23 ldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq 62 (264)
T KOG1702|consen 23 LDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQ 62 (264)
T ss_pred HHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccc
Confidence 4678999999999999999888887788999999999753
No 20
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=94.41 E-value=0.016 Score=53.01 Aligned_cols=40 Identities=23% Similarity=0.561 Sum_probs=34.4
Q ss_pred CCcccCCCeeecCCCCCCCCCceeecCCcccccccccccc
Q 019740 2 EAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQH 41 (336)
Q Consensus 2 g~~wH~~CF~C~~C~~~L~~~~F~~~dg~~yC~~CY~~~~ 41 (336)
+..||..||+|..|+..|+...+...++.+||+..+.+++
T Consensus 128 ~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~ 167 (200)
T KOG1700|consen 128 GLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLF 167 (200)
T ss_pred hhhhhhhheeecccccccCCcchhhcCCccccchhhheee
Confidence 5679999999999999999999999899999877655543
No 21
>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=86.47 E-value=0.63 Score=42.78 Aligned_cols=38 Identities=26% Similarity=0.300 Sum_probs=31.6
Q ss_pred hhhhhhHHHHHHHHHHHhcCCCCCCcchhhhHHHHHHHH
Q 019740 224 LLTGSILAHEMMHAWLRLKGYPNLRPDVEEGICQVLAHM 262 (336)
Q Consensus 224 ~~~~~~lahe~~ha~l~~~g~~~l~~~veeg~cq~~a~~ 262 (336)
--.-.+|-|||+|+|+.- |...-|.-+-|||...+-+.
T Consensus 94 ~Ei~Gvl~HE~~H~~Q~~-~~~~~P~~liEGIADyVRl~ 131 (205)
T PF04450_consen 94 DEIIGVLYHEMVHCWQWD-GRGTAPGGLIEGIADYVRLK 131 (205)
T ss_pred HHHHHHHHHHHHHHhhcC-CCCCCChhheecHHHHHHHH
Confidence 445689999999999987 45578899999999988655
No 22
>PF14891 Peptidase_M91: Effector protein
Probab=82.10 E-value=0.9 Score=40.35 Aligned_cols=20 Identities=30% Similarity=0.441 Sum_probs=17.2
Q ss_pred hhhhhHHHHHHHHHHHhcCC
Q 019740 225 LTGSILAHEMMHAWLRLKGY 244 (336)
Q Consensus 225 ~~~~~lahe~~ha~l~~~g~ 244 (336)
.--.+|+|||.|||=.++|-
T Consensus 102 ~p~v~L~HEL~HA~~~~~Gt 121 (174)
T PF14891_consen 102 PPFVVLYHELIHAYDYMNGT 121 (174)
T ss_pred HHHHHHHHHHHHHHHHHCCC
Confidence 34589999999999999985
No 23
>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=81.37 E-value=2.1 Score=38.74 Aligned_cols=45 Identities=20% Similarity=0.171 Sum_probs=34.6
Q ss_pred hhhhhhHHHHHHHHHHHh------cCCCCCCcchhhhHHHHHHHHhhhccc
Q 019740 224 LLTGSILAHEMMHAWLRL------KGYPNLRPDVEEGICQVLAHMWLESEI 268 (336)
Q Consensus 224 ~~~~~~lahe~~ha~l~~------~g~~~l~~~veeg~cq~~a~~wl~~~~ 268 (336)
-..-+++|||+-|++-.- .+...|+..|=||+.+..+..-+....
T Consensus 63 ~~l~~~iaHE~hH~~r~~~~~~~~~~~TLld~~I~EGlAe~f~~~~~g~~~ 113 (195)
T PF10026_consen 63 EELPALIAHEYHHNCRYEQIGWDPEDTTLLDSLIMEGLAEYFAEELYGEEY 113 (195)
T ss_pred HHHHHHHHHHHHHHHHHhccCCCCCCCCHHHHHHHhhHHHHHHHHHcCCCC
Confidence 456789999999997433 244567789999999999988766644
No 24
>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=81.36 E-value=0.74 Score=45.11 Aligned_cols=43 Identities=26% Similarity=0.333 Sum_probs=31.7
Q ss_pred hhhhHHHHHHHHHHHhc-CCCCC-CcchhhhHHHHHHHHhhhccc
Q 019740 226 TGSILAHEMMHAWLRLK-GYPNL-RPDVEEGICQVLAHMWLESEI 268 (336)
Q Consensus 226 ~~~~lahe~~ha~l~~~-g~~~l-~~~veeg~cq~~a~~wl~~~~ 268 (336)
...++|||++|-|+--- ....- +..+-||+++.++++|++.-.
T Consensus 295 ~~~~iahElahqWfGn~vt~~~w~d~WL~Eg~a~y~~~~~~~~~~ 339 (390)
T PF01433_consen 295 IASLIAHELAHQWFGNLVTPKWWSDLWLNEGFATYLEYLILEKLF 339 (390)
T ss_dssp HHHHHHHHHHTTTBTTTEEESSGGGHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHhccCCccccchhhhHHHHHHHHHHHHhHhhcc
Confidence 45789999999996421 11111 256999999999999999865
No 25
>PF01431 Peptidase_M13: Peptidase family M13 This is family M13 in the peptidase classification. ; InterPro: IPR018497 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 M13 (neprilysin family, clan MA(E)). 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 []. M13 peptidases are well-studied proteases found in a wide range of organisms including mammals and bacteria. In mammals they participate in processes such as cardiovascular development, blood-pressure regulation, nervous control of respiration, and regulation of the function of neuropeptides in the central nervous system. In bacteria they may be used for digestion of milk [, ]. The family includes eukaryotic and prokaryotic oligopeptidases, as well as some of the proteins responsible for the molecular basis of the blood group antigens e.g. Kell []. Neprilysin (3.4.24.11 from EC), is another member of this group, it is variously known as common acute lymphoblastic leukemia antigen (CALLA), enkephalinase (gp100) and neutral endopeptidase metalloendopeptidase (NEP). It is a plasma membrane-bound mammalian enzyme that is able to digest biologically-active peptides, including enkephalins []. The zinc ligands of neprilysin are known and are analogous to those in thermolysin, a related peptidase [, ]. Neprilysins, like thermolysin, are inhibited by phosphoramidon, which appears to selectively inhibit this family in mammals. The enzymes are all oligopeptidases, digesting oligo- and polypeptides, but not proteins []. Neprilysin consists of a short cytoplasmic domain, a membrane-spanning region and a large extracellular domain. The cytoplasmic domain contains a conformationally-restrained octapeptide, which is thought to act as a stop transfer sequence that prevents proteolysis and secretion [, ].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2QPJ_A 1R1I_A 1R1J_A 1Y8J_A 1R1H_A 1DMT_A 2YB9_A 3DWB_A 3ZUK_A.
Probab=79.66 E-value=0.68 Score=41.68 Aligned_cols=17 Identities=53% Similarity=0.579 Sum_probs=14.5
Q ss_pred hhhhhHHHHHHHHHHHh
Q 019740 225 LTGSILAHEMMHAWLRL 241 (336)
Q Consensus 225 ~~~~~lahe~~ha~l~~ 241 (336)
..|+||||||+||+-..
T Consensus 35 ~lG~ilahel~hafd~~ 51 (206)
T PF01431_consen 35 GLGFILAHELMHAFDPE 51 (206)
T ss_dssp THHHHHHHHHHHCTSTT
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 47999999999999654
No 26
>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=78.34 E-value=2.4 Score=33.59 Aligned_cols=52 Identities=23% Similarity=0.150 Sum_probs=34.2
Q ss_pred EEEEEecCCChhhhhhhHHHHHHHHHHHhcCC------CCCCcchhhhHHHHHHHHhh
Q 019740 213 TAILILYGLPRLLTGSILAHEMMHAWLRLKGY------PNLRPDVEEGICQVLAHMWL 264 (336)
Q Consensus 213 ~~ilvl~glp~~~~~~~lahe~~ha~l~~~g~------~~l~~~veeg~cq~~a~~wl 264 (336)
.-|+|=..++..-.-.++|||++|.++.-.+. ........|=-++..|...|
T Consensus 29 ~~I~in~~~~~~~~~f~laHELgH~~~~~~~~~~~~~~~~~~~~~~E~~An~fA~~lL 86 (122)
T PF06114_consen 29 PIIFINSNLSPERQRFTLAHELGHILLHHGDETFNYYLNYFFNERQEREANAFAAALL 86 (122)
T ss_dssp TEEEEESSS-HHHHHHHHHHHHHHHHHHH-HHHHHHHHHH--THHHHHHHHHHHHHHH
T ss_pred CEEEECCCCCHHHHHHHHHHHHHHHHhhhccccchhhccccchhhHHHHHHHHHHHHh
Confidence 45778888999999999999999999988641 23344445555555554443
No 27
>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=77.22 E-value=1.5 Score=37.64 Aligned_cols=22 Identities=32% Similarity=0.150 Sum_probs=19.6
Q ss_pred CChhhhhhhHHHHHHHHHHHhc
Q 019740 221 LPRLLTGSILAHEMMHAWLRLK 242 (336)
Q Consensus 221 lp~~~~~~~lahe~~ha~l~~~ 242 (336)
.|.-..-.+|+|||.|||+.+.
T Consensus 55 ~~~~~~~~tL~HEm~H~~~~~~ 76 (157)
T PF10263_consen 55 NPEEELIDTLLHEMAHAAAYVF 76 (157)
T ss_pred hHHHHHHHHHHHHHHHHHhhhc
Confidence 5677888999999999999887
No 28
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.39 E-value=1.1 Score=40.36 Aligned_cols=49 Identities=18% Similarity=0.497 Sum_probs=38.8
Q ss_pred CCCeeecCCCCCCCCCc-eeecCCccccccccccc--cCCcCcccCCcccCC
Q 019740 7 PECFRCHSCNLPITDVE-FSMSGNRPYHKHCYKEQ--HHPKCDVCQNFIPTN 55 (336)
Q Consensus 7 ~~CF~C~~C~~~L~~~~-F~~~dg~~yC~~CY~~~--~~pkC~~C~~~I~~~ 55 (336)
..||+|..|=....... +..+=|.+||+.|-++. ...+|..|++.|...
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k 180 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHK 180 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccchh
Confidence 35889999977766544 66788999999999863 567999999988754
No 29
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=73.98 E-value=2 Score=33.39 Aligned_cols=18 Identities=33% Similarity=0.564 Sum_probs=14.3
Q ss_pred hhhhHHHHHHHHHHHhcC
Q 019740 226 TGSILAHEMMHAWLRLKG 243 (336)
Q Consensus 226 ~~~~lahe~~ha~l~~~g 243 (336)
.-.+||||++|++..-.|
T Consensus 61 ~~~llaHEl~Hv~Qq~~g 78 (79)
T PF13699_consen 61 GRALLAHELAHVVQQRRG 78 (79)
T ss_pred cchhHhHHHHHHHhhccC
Confidence 457999999999876543
No 30
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=73.32 E-value=3.4 Score=31.15 Aligned_cols=47 Identities=15% Similarity=0.318 Sum_probs=24.8
Q ss_pred eeecCCCCCCCCCceeecCCccccccccccccCCcCcccCCcccCCC
Q 019740 10 FRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNS 56 (336)
Q Consensus 10 F~C~~C~~~L~~~~F~~~dg~~yC~~CY~~~~~pkC~~C~~~I~~~~ 56 (336)
++|..|..-|...-....=...||..|-.+.++..|.+|+.|-..++
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 47888988776532333456899999999989999999999987654
No 31
>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=71.84 E-value=4.5 Score=40.44 Aligned_cols=41 Identities=24% Similarity=0.250 Sum_probs=30.7
Q ss_pred hhhhhHHHHHHHHH---HH--hcCC-CCCCcchhhhHHHHHHHHhhh
Q 019740 225 LTGSILAHEMMHAW---LR--LKGY-PNLRPDVEEGICQVLAHMWLE 265 (336)
Q Consensus 225 ~~~~~lahe~~ha~---l~--~~g~-~~l~~~veeg~cq~~a~~wl~ 265 (336)
.+-++||||++|.= .| +.|- ..-+..+|||+-+++.++--.
T Consensus 138 ~~~sTlAHEfQHmInfy~~~v~~g~~~~~dtWLnE~lS~~aEdl~s~ 184 (366)
T PF10460_consen 138 TVYSTLAHEFQHMINFYQRGVLHGKQYAMDTWLNEMLSMSAEDLYSS 184 (366)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCcccccHHHHHHHHHHHHHHhc
Confidence 46799999999964 33 2342 357899999999999887533
No 32
>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=71.66 E-value=2.8 Score=33.38 Aligned_cols=29 Identities=24% Similarity=0.617 Sum_probs=23.5
Q ss_pred eecCCCCCCCCCceee-cCCcccccccccc
Q 019740 11 RCHSCNLPITDVEFSM-SGNRPYHKHCYKE 39 (336)
Q Consensus 11 ~C~~C~~~L~~~~F~~-~dg~~yC~~CY~~ 39 (336)
.|..|+++|....|.. .+|..+|..|..+
T Consensus 80 ~C~vC~k~l~~~~f~~~p~~~v~H~~C~~r 109 (109)
T PF10367_consen 80 KCSVCGKPLGNSVFVVFPCGHVVHYSCIKR 109 (109)
T ss_pred CccCcCCcCCCceEEEeCCCeEEecccccC
Confidence 5899999999877776 5678899888753
No 33
>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=71.21 E-value=1.1 Score=30.03 Aligned_cols=33 Identities=18% Similarity=0.361 Sum_probs=22.5
Q ss_pred CcccCCcccCCCCceEEEeeecccccccCCCCcCCCCCccCCCCccC
Q 019740 45 CDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERME 91 (336)
Q Consensus 45 C~~C~~~I~~~~~g~i~~~~~~fW~qkyCp~H~H~~CF~C~~C~~~l 91 (336)
|+.|+++|.+++ -++.+.++.| + |.|.+|.+.|
T Consensus 1 Cd~CG~~I~~eP-~~~k~~~~~y----------~---fCC~tC~~~f 33 (37)
T PF08394_consen 1 CDYCGGEITGEP-IVVKIGNKVY----------Y---FCCPTCLSQF 33 (37)
T ss_pred CCccCCcccCCE-EEEEECCeEE----------E---EECHHHHHHH
Confidence 788999999875 2334455554 2 7778887665
No 34
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=70.06 E-value=3.3 Score=35.64 Aligned_cols=23 Identities=39% Similarity=0.288 Sum_probs=18.2
Q ss_pred CChhhhhhhHHHHHHHHHHHhcC
Q 019740 221 LPRLLTGSILAHEMMHAWLRLKG 243 (336)
Q Consensus 221 lp~~~~~~~lahe~~ha~l~~~g 243 (336)
.|...+-.+|.|||.|++..+.|
T Consensus 54 ~~~~~l~~~l~HEm~H~~~~~~g 76 (146)
T smart00731 54 NGRDRLRETLLHELCHAALYLFG 76 (146)
T ss_pred ccHHHHHhhHHHHHHHHHHHHhC
Confidence 34556677999999999998754
No 35
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=69.30 E-value=0.59 Score=42.94 Aligned_cols=58 Identities=12% Similarity=0.244 Sum_probs=39.5
Q ss_pred CcCcccCCcccCCCCceEEEeeecccccccCCCCcCCCCCccCCCCccCCCCCceEEcCCCceeccchhhhc
Q 019740 43 PKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSA 114 (336)
Q Consensus 43 pkC~~C~~~I~~~~~g~i~~~~~~fW~qkyCp~H~H~~CF~C~~C~~~l~~~~~f~~~~dG~~yC~~C~~~~ 114 (336)
+.|..|++.+.+-+ .+.-.++ +| |..||+|..|+..|. -.+|-.. |.++||-..|.+.
T Consensus 5 ~n~~~cgk~vYPvE--~v~cldk-~w---------hk~cfkce~c~mtln-mKnyKgy-~kkpycn~hYpkq 62 (264)
T KOG1702|consen 5 CNREDCGKTVYPVE--EVKCLDK-VW---------HKQCFKCEVCGMTLN-MKNYKGY-DKKPYCNPHYPKQ 62 (264)
T ss_pred chhhhhccccccHH--HHhhHHH-HH---------HHHhheeeeccCChh-hhhcccc-ccCCCcCcccccc
Confidence 45667777665432 2333343 35 999999999999885 3444333 7899999998764
No 36
>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=69.21 E-value=4.7 Score=44.40 Aligned_cols=40 Identities=18% Similarity=0.286 Sum_probs=29.9
Q ss_pred hhhHHHHHHHHHHH-hcCCC-CCCcchhhhHHHHHHHHhhhc
Q 019740 227 GSILAHEMMHAWLR-LKGYP-NLRPDVEEGICQVLAHMWLES 266 (336)
Q Consensus 227 ~~~lahe~~ha~l~-~~g~~-~l~~~veeg~cq~~a~~wl~~ 266 (336)
..++|||++|-|.- |-... -=+..+-||+...++++|++.
T Consensus 288 ~~viaHElAHqWFGnlVT~~wW~dlWLnEGFAty~e~~~~~~ 329 (831)
T TIGR02412 288 AGVILHEMAHMWFGDLVTMRWWNDLWLNESFAEYMGTLASAE 329 (831)
T ss_pred HHHHHHHHHHHHhCCEeccccccchhHHHHHHHHHHHHHHHh
Confidence 47999999999974 11111 123678999999999999875
No 37
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=66.80 E-value=5.8 Score=42.61 Aligned_cols=38 Identities=21% Similarity=0.603 Sum_probs=28.4
Q ss_pred eecCCCCCCCCCceeecCCccccccccccccCCcCcccCCcccCC
Q 019740 11 RCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTN 55 (336)
Q Consensus 11 ~C~~C~~~L~~~~F~~~dg~~yC~~CY~~~~~pkC~~C~~~I~~~ 55 (336)
+|..|+.... ++..||..|-..+....|..|+..+...
T Consensus 3 ~Cp~Cg~~n~-------~~akFC~~CG~~l~~~~Cp~CG~~~~~~ 40 (645)
T PRK14559 3 ICPQCQFENP-------NNNRFCQKCGTSLTHKPCPQCGTEVPVD 40 (645)
T ss_pred cCCCCCCcCC-------CCCccccccCCCCCCCcCCCCCCCCCcc
Confidence 6888887753 3455788888776667899999987754
No 38
>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=65.39 E-value=3.7 Score=31.47 Aligned_cols=57 Identities=16% Similarity=0.359 Sum_probs=32.2
Q ss_pred eecCCCCCCCCCceeecCCccccccccccc-cCCcCcccCCcccCCCCceEEEee-ecccccccCCCCcCCCCCccCCCC
Q 019740 11 RCHSCNLPITDVEFSMSGNRPYHKHCYKEQ-HHPKCDVCQNFIPTNSAGLIEYRA-HPFWLQKYCPSHERDGTPRCCSCE 88 (336)
Q Consensus 11 ~C~~C~~~L~~~~F~~~dg~~yC~~CY~~~-~~pkC~~C~~~I~~~~~g~i~~~~-~~fW~qkyCp~H~H~~CF~C~~C~ 88 (336)
.|..|+.+|... ++..+|..|.... ..+.|..|++++. ++.+=| .. |.|..|+
T Consensus 3 ~CP~C~~~L~~~-----~~~~~C~~C~~~~~~~a~CPdC~~~Le-----~LkACGAvd---------------YFC~~c~ 57 (70)
T PF07191_consen 3 TCPKCQQELEWQ-----GGHYHCEACQKDYKKEAFCPDCGQPLE-----VLKACGAVD---------------YFCNHCH 57 (70)
T ss_dssp B-SSS-SBEEEE-----TTEEEETTT--EEEEEEE-TTT-SB-E-----EEEETTEEE---------------EE-TTTT
T ss_pred cCCCCCCccEEe-----CCEEECccccccceecccCCCcccHHH-----HHHHhcccc---------------eeeccCC
Confidence 588898888653 3778888887652 3468999999987 466655 33 3588888
Q ss_pred ccCC
Q 019740 89 RMEP 92 (336)
Q Consensus 89 ~~l~ 92 (336)
.++.
T Consensus 58 gLiS 61 (70)
T PF07191_consen 58 GLIS 61 (70)
T ss_dssp -EE-
T ss_pred ceee
Confidence 7664
No 39
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=63.27 E-value=3.9 Score=39.57 Aligned_cols=45 Identities=18% Similarity=0.364 Sum_probs=34.8
Q ss_pred eeecCCCCCCCCCceeecCCcccccccccccc--CCcCcccCCcccCC
Q 019740 10 FRCHSCNLPITDVEFSMSGNRPYHKHCYKEQH--HPKCDVCQNFIPTN 55 (336)
Q Consensus 10 F~C~~C~~~L~~~~F~~~dg~~yC~~CY~~~~--~pkC~~C~~~I~~~ 55 (336)
|.|..|++++.. .-...-+..||+.|..+.+ +++|.+|++.+.+.
T Consensus 242 f~c~icr~~f~~-pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~ 288 (313)
T KOG1813|consen 242 FKCFICRKYFYR-PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHGS 288 (313)
T ss_pred cccccccccccc-chhhcCCceeehhhhccccccCCcceecccccccc
Confidence 778888888765 3444667899999997755 47999999998874
No 40
>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=61.75 E-value=4.5 Score=36.28 Aligned_cols=19 Identities=26% Similarity=0.354 Sum_probs=14.7
Q ss_pred hhhhhhhHHHHHHHHHHHh
Q 019740 223 RLLTGSILAHEMMHAWLRL 241 (336)
Q Consensus 223 ~~~~~~~lahe~~ha~l~~ 241 (336)
+....-+|+|||.|||=.+
T Consensus 68 ~~~l~~~l~HELIHayD~c 86 (173)
T PF09768_consen 68 QGHLEDTLTHELIHAYDHC 86 (173)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3445689999999999544
No 41
>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=61.67 E-value=4.9 Score=35.12 Aligned_cols=18 Identities=28% Similarity=0.379 Sum_probs=12.3
Q ss_pred ChhhhhhhHHHHHHHHHH
Q 019740 222 PRLLTGSILAHEMMHAWL 239 (336)
Q Consensus 222 p~~~~~~~lahe~~ha~l 239 (336)
|....-=|+||||+|+..
T Consensus 131 ~~~~~lDVvaHEltHGVt 148 (150)
T PF01447_consen 131 PFASSLDVVAHELTHGVT 148 (150)
T ss_dssp -GGG-HHHHHHHHHHHHH
T ss_pred cCccccceeeeccccccc
Confidence 333335799999999864
No 42
>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=60.31 E-value=5.6 Score=28.54 Aligned_cols=45 Identities=13% Similarity=0.214 Sum_probs=34.6
Q ss_pred eeecCCCCCCCCCceeecCCcccccccccccc--CCcCcccCCcccCC
Q 019740 10 FRCHSCNLPITDVEFSMSGNRPYHKHCYKEQH--HPKCDVCQNFIPTN 55 (336)
Q Consensus 10 F~C~~C~~~L~~~~F~~~dg~~yC~~CY~~~~--~pkC~~C~~~I~~~ 55 (336)
|.|..|+..+.+ ......|..||+.|..+.. ...|..|++++...
T Consensus 2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~ 48 (63)
T smart00504 2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHE 48 (63)
T ss_pred cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChh
Confidence 678999999876 3455678999999987532 46799999988654
No 43
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=60.00 E-value=5.5 Score=29.49 Aligned_cols=37 Identities=22% Similarity=0.499 Sum_probs=19.1
Q ss_pred eecCCCCCCCCCceeecCCccccccccccccCCcCcccCCc
Q 019740 11 RCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNF 51 (336)
Q Consensus 11 ~C~~C~~~L~~~~F~~~dg~~yC~~CY~~~~~pkC~~C~~~ 51 (336)
+|..|+.+|...+-+ -...|..|-+. .-.||..|.+.
T Consensus 9 ~CtSCg~~i~~~~~~---~~F~CPnCG~~-~I~RC~~CRk~ 45 (59)
T PRK14890 9 KCTSCGIEIAPREKA---VKFLCPNCGEV-IIYRCEKCRKQ 45 (59)
T ss_pred cccCCCCcccCCCcc---CEeeCCCCCCe-eEeechhHHhc
Confidence 567777777654311 13456666432 23345555553
No 44
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=59.86 E-value=16 Score=33.81 Aligned_cols=55 Identities=25% Similarity=0.131 Sum_probs=39.9
Q ss_pred EEEEEecCCChhhhhhhHHHHHHHHHHHhcC------CCC-CCcchhhhHHHHHHHHhhhcc
Q 019740 213 TAILILYGLPRLLTGSILAHEMMHAWLRLKG------YPN-LRPDVEEGICQVLAHMWLESE 267 (336)
Q Consensus 213 ~~ilvl~glp~~~~~~~lahe~~ha~l~~~g------~~~-l~~~veeg~cq~~a~~wl~~~ 267 (336)
.-|++-.-.+...-.=+||||+.|++|--.+ .++ -....-|--|+.+|-.-|-..
T Consensus 59 ~~I~iN~n~~~~r~rFtlAHELGH~llH~~~~~~~~~~~~~~~~~~~E~~AN~FAa~lLmP~ 120 (213)
T COG2856 59 PVIYINANNSLERKRFTLAHELGHALLHTDLNTRFDAEPTLQQDRKIEAEANAFAAELLMPE 120 (213)
T ss_pred ceEEEeCCCCHHHHHHHHHHHHhHHHhccccchhhhcccccchhHHHHHHHHHHHHHHhCCh
Confidence 4566666678888888999999999987654 122 224456778999988877654
No 45
>PRK04351 hypothetical protein; Provisional
Probab=59.59 E-value=6.8 Score=34.23 Aligned_cols=22 Identities=32% Similarity=0.342 Sum_probs=17.5
Q ss_pred ChhhhhhhHHHHHHHHHHHhcC
Q 019740 222 PRLLTGSILAHEMMHAWLRLKG 243 (336)
Q Consensus 222 p~~~~~~~lahe~~ha~l~~~g 243 (336)
+.-.+..||+|||.|..+.+.|
T Consensus 57 ~~~~l~~vv~HElcH~~~~~~g 78 (149)
T PRK04351 57 GLEELIGIIKHELCHYHLHLEG 78 (149)
T ss_pred cHHHHHhhHHHHHHHHHHHHHC
Confidence 3445578999999999998864
No 46
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=59.34 E-value=5.1 Score=34.37 Aligned_cols=23 Identities=22% Similarity=0.648 Sum_probs=18.1
Q ss_pred eecCCCCCCCCCceeecCCccccccccc
Q 019740 11 RCHSCNLPITDVEFSMSGNRPYHKHCYK 38 (336)
Q Consensus 11 ~C~~C~~~L~~~~F~~~dg~~yC~~CY~ 38 (336)
.|..|+.|| |- ++|.+||.-|-.
T Consensus 30 hCp~Cg~PL----F~-KdG~v~CPvC~~ 52 (131)
T COG1645 30 HCPKCGTPL----FR-KDGEVFCPVCGY 52 (131)
T ss_pred hCcccCCcc----ee-eCCeEECCCCCc
Confidence 378899988 44 899999888764
No 47
>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=58.99 E-value=5.2 Score=27.83 Aligned_cols=43 Identities=21% Similarity=0.499 Sum_probs=30.5
Q ss_pred eecCCCCCCCCCceeecCCcc-ccccccccc--cCCcCcccCCcccC
Q 019740 11 RCHSCNLPITDVEFSMSGNRP-YHKHCYKEQ--HHPKCDVCQNFIPT 54 (336)
Q Consensus 11 ~C~~C~~~L~~~~F~~~dg~~-yC~~CY~~~--~~pkC~~C~~~I~~ 54 (336)
.|..|.....+. .+..=|.. +|..|..+. ...+|..|+++|..
T Consensus 4 ~C~iC~~~~~~~-~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 4 ECPICFENPRDV-VLLPCGHLCFCEECAERLLKRKKKCPICRQPIES 49 (50)
T ss_dssp B-TTTSSSBSSE-EEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-SE
T ss_pred CCccCCccCCce-EEeCCCChHHHHHHhHHhcccCCCCCcCChhhcC
Confidence 577777776553 33455777 999999876 56899999999863
No 48
>PF12773 DZR: Double zinc ribbon
Probab=58.80 E-value=9.3 Score=26.47 Aligned_cols=11 Identities=27% Similarity=0.773 Sum_probs=5.1
Q ss_pred ceeccchhhhc
Q 019740 104 RKLCLECLDSA 114 (336)
Q Consensus 104 ~~yC~~C~~~~ 114 (336)
..+|..|...+
T Consensus 29 ~~~C~~Cg~~~ 39 (50)
T PF12773_consen 29 KKICPNCGAEN 39 (50)
T ss_pred CCCCcCCcCCC
Confidence 34455554443
No 49
>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=58.10 E-value=5.7 Score=37.23 Aligned_cols=18 Identities=28% Similarity=0.486 Sum_probs=15.7
Q ss_pred CChhhhhhhHHHHHHHHH
Q 019740 221 LPRLLTGSILAHEMMHAW 238 (336)
Q Consensus 221 lp~~~~~~~lahe~~ha~ 238 (336)
+|...+..++||||+|.+
T Consensus 162 ~~~~~~a~t~AHElGHnl 179 (244)
T cd04270 162 VPTKESDLVTAHELGHNF 179 (244)
T ss_pred cchhHHHHHHHHHHHHhc
Confidence 577778899999999987
No 50
>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=57.97 E-value=8.2 Score=34.56 Aligned_cols=29 Identities=31% Similarity=0.334 Sum_probs=21.5
Q ss_pred EEEEecC----CChhhhhhhHHHHHHHHHHHhc
Q 019740 214 AILILYG----LPRLLTGSILAHEMMHAWLRLK 242 (336)
Q Consensus 214 ~ilvl~g----lp~~~~~~~lahe~~ha~l~~~ 242 (336)
.|+|-.| +++--..+|||||++|...+-.
T Consensus 73 ~I~v~~~ll~~~~~~el~aVlaHElgH~~~~h~ 105 (226)
T PF01435_consen 73 RIVVTSGLLESLSEDELAAVLAHELGHIKHRHI 105 (226)
T ss_dssp EEEEEHHHHHHSSHHHHHHHHHHHHHHHHTTHC
T ss_pred EEEEeChhhhcccHHHHHHHHHHHHHHHHcCCc
Confidence 4555555 5666677999999999997763
No 51
>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=57.05 E-value=8.9 Score=30.38 Aligned_cols=27 Identities=15% Similarity=0.540 Sum_probs=16.0
Q ss_pred cCCCCccCCCCCceEEcCCCceeccchh
Q 019740 84 CCSCERMEPRDTKYLSLDDGRKLCLECL 111 (336)
Q Consensus 84 C~~C~~~l~~~~~f~~~~dG~~yC~~C~ 111 (336)
|..|+++|. +..|+..++|..+...|.
T Consensus 81 C~vC~k~l~-~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 81 CSVCGKPLG-NSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred ccCcCCcCC-CceEEEeCCCeEEecccc
Confidence 666666664 455666666666655554
No 52
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=57.01 E-value=3.4 Score=29.56 Aligned_cols=29 Identities=24% Similarity=0.507 Sum_probs=23.1
Q ss_pred eecCCCCCCCCCc-eeecCCccccccccccc
Q 019740 11 RCHSCNLPITDVE-FSMSGNRPYHKHCYKEQ 40 (336)
Q Consensus 11 ~C~~C~~~L~~~~-F~~~dg~~yC~~CY~~~ 40 (336)
.|+.|+..+.-.. |-..|| ..|.+|+.++
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 4899999997533 667888 7999999875
No 53
>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=56.02 E-value=7.4 Score=26.64 Aligned_cols=22 Identities=23% Similarity=0.690 Sum_probs=15.9
Q ss_pred eecCCCCCCCCCceeecCCccccccc
Q 019740 11 RCHSCNLPITDVEFSMSGNRPYHKHC 36 (336)
Q Consensus 11 ~C~~C~~~L~~~~F~~~dg~~yC~~C 36 (336)
.|..|+.||- -.++|+.||..|
T Consensus 19 ~Cp~C~~PL~----~~k~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPLM----RDKDGKIYCVSC 40 (41)
T ss_pred ccCCCCCeeE----EecCCCEECCCC
Confidence 4677887773 347888888776
No 54
>PHA02456 zinc metallopeptidase motif-containing protein
Probab=53.85 E-value=7.8 Score=32.47 Aligned_cols=17 Identities=47% Similarity=0.761 Sum_probs=13.1
Q ss_pred hhHHHHHHHHHHHhc-CC
Q 019740 228 SILAHEMMHAWLRLK-GY 244 (336)
Q Consensus 228 ~~lahe~~ha~l~~~-g~ 244 (336)
-.||||+.|+|..-. |+
T Consensus 81 ~TL~HEL~H~WQ~RsYG~ 98 (141)
T PHA02456 81 DTLAHELNHAWQFRTYGL 98 (141)
T ss_pred HHHHHHHHHHHhhhccce
Confidence 579999999996543 54
No 55
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=53.17 E-value=8.1 Score=28.14 Aligned_cols=39 Identities=23% Similarity=0.629 Sum_probs=23.0
Q ss_pred eecCCCCCCCCC-ce--eecCCccccccccccccCCcCcc--cCCc
Q 019740 11 RCHSCNLPITDV-EF--SMSGNRPYHKHCYKEQHHPKCDV--CQNF 51 (336)
Q Consensus 11 ~C~~C~~~L~~~-~F--~~~dg~~yC~~CY~~~~~pkC~~--C~~~ 51 (336)
+|..|+++|.+. .- -..=|-||+++||.+ .-.|.. |+.+
T Consensus 7 ~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~--~g~C~~~~c~~~ 50 (54)
T PF14446_consen 7 KCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK--AGGCINYSCGTG 50 (54)
T ss_pred cChhhCCcccCCCCEEECCCCCCcccHHHHhh--CCceEeccCCCC
Confidence 578888888421 12 223477888888864 334544 4443
No 56
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=52.92 E-value=7.4 Score=26.41 Aligned_cols=39 Identities=21% Similarity=0.524 Sum_probs=27.7
Q ss_pred ecCCCCCCC-CCcee-ecCCcccccccccccc--CCcCcccCC
Q 019740 12 CHSCNLPIT-DVEFS-MSGNRPYHKHCYKEQH--HPKCDVCQN 50 (336)
Q Consensus 12 C~~C~~~L~-~~~F~-~~dg~~yC~~CY~~~~--~pkC~~C~~ 50 (336)
|..|...+. ...+. ..=|..+|..|..++. ..+|..|++
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 677878873 22343 4558999999998877 667887764
No 57
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.66 E-value=6.2 Score=35.61 Aligned_cols=51 Identities=24% Similarity=0.540 Sum_probs=39.0
Q ss_pred CCCCCccCCCCccCCCCCceEEcCCCceeccchhhhcccCCCCCCchhhHHH
Q 019740 78 RDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQ 129 (336)
Q Consensus 78 H~~CF~C~~C~~~l~~~~~f~~~~dG~~yC~~C~~~~v~~~~~C~~c~~~I~ 129 (336)
-..||+|-.|--....... +.-+=|.++|..|...++..+..|--|.+.|.
T Consensus 128 ~~~~~~CPiCl~~~sek~~-vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVP-VSTKCGHVFCSQCIKDALKNTNKCPTCRKKIT 178 (187)
T ss_pred cccccCCCceecchhhccc-cccccchhHHHHHHHHHHHhCCCCCCcccccc
Confidence 4678999999766532222 23346999999999999999999999987774
No 58
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=52.38 E-value=8.5 Score=27.49 Aligned_cols=30 Identities=23% Similarity=0.713 Sum_probs=21.8
Q ss_pred ccCCCCccCCCCCceEEcCCCceeccchhhhc
Q 019740 83 RCCSCERMEPRDTKYLSLDDGRKLCLECLDSA 114 (336)
Q Consensus 83 ~C~~C~~~l~~~~~f~~~~dG~~yC~~C~~~~ 114 (336)
.|..|+..++.-.++ -+.|| .+|..|+.++
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 488899887644443 46688 6899999885
No 59
>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=52.28 E-value=5.2 Score=35.24 Aligned_cols=54 Identities=15% Similarity=0.394 Sum_probs=35.6
Q ss_pred CccccccccccccCCcCcccCCcccCCC--CceEEEeeecccccccCCCCcCCCCCccCCCCccCCCCC
Q 019740 29 NRPYHKHCYKEQHHPKCDVCQNFIPTNS--AGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDT 95 (336)
Q Consensus 29 g~~yC~~CY~~~~~pkC~~C~~~I~~~~--~g~i~~~~~~fW~qkyCp~H~H~~CF~C~~C~~~l~~~~ 95 (336)
..-||.+|-.+ .-..|..|+.+|.|.. +|++.+. ..| +.-- -|..||+++|+..
T Consensus 27 ~~~fC~kCG~~-tI~~Cp~C~~~IrG~y~v~gv~~~g-~~~----------~~Ps-YC~~CGkpyPWt~ 82 (158)
T PF10083_consen 27 REKFCSKCGAK-TITSCPNCSTPIRGDYHVEGVFGLG-GHY----------EAPS-YCHNCGKPYPWTE 82 (158)
T ss_pred HHHHHHHhhHH-HHHHCcCCCCCCCCceecCCeeeeC-CCC----------CCCh-hHHhCCCCCchHH
Confidence 46789999876 4568999999999863 1333332 221 3222 3899999998544
No 60
>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=50.47 E-value=15 Score=32.79 Aligned_cols=24 Identities=29% Similarity=0.252 Sum_probs=18.7
Q ss_pred EEEEecCCChhhhhhhHHHHHHHH
Q 019740 214 AILILYGLPRLLTGSILAHEMMHA 237 (336)
Q Consensus 214 ~ilvl~glp~~~~~~~lahe~~ha 237 (336)
+|....+..-+.++.++|||++|.
T Consensus 119 ~i~~~~~~~~~~~a~~~AHelGH~ 142 (199)
T PF01421_consen 119 GIVEDHSRSGLSFAVIIAHELGHN 142 (199)
T ss_dssp EEEE-SSSSHHHHHHHHHHHHHHH
T ss_pred cEeeeccchhHHHHHHHHHHHHHh
Confidence 555555677888999999999995
No 61
>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=50.20 E-value=8.3 Score=25.58 Aligned_cols=26 Identities=19% Similarity=0.322 Sum_probs=18.9
Q ss_pred eeecCCCCCCCCCceeecCCcccccccccc
Q 019740 10 FRCHSCNLPITDVEFSMSGNRPYHKHCYKE 39 (336)
Q Consensus 10 F~C~~C~~~L~~~~F~~~dg~~yC~~CY~~ 39 (336)
+.|..|+.. .|...||..||..|-.+
T Consensus 9 ~~C~~C~~~----~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSR----WFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCe----EeEccCCEEEhhhCceE
Confidence 347777654 57778999999888643
No 62
>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=48.07 E-value=1.9 Score=28.31 Aligned_cols=28 Identities=18% Similarity=0.487 Sum_probs=21.7
Q ss_pred ecCCCCCCCCCceeecCCcccccccccc
Q 019740 12 CHSCNLPITDVEFSMSGNRPYHKHCYKE 39 (336)
Q Consensus 12 C~~C~~~L~~~~F~~~dg~~yC~~CY~~ 39 (336)
|..|+.+|........++..+|.+|..+
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~C~~C~~~ 33 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATLCVECQER 33 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS-HHHHHH
T ss_pred ccccCChHHHHHHHhCCCcEECHHHhCc
Confidence 8999999988777777889999998754
No 63
>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=48.01 E-value=5.9 Score=25.54 Aligned_cols=40 Identities=13% Similarity=0.404 Sum_probs=24.6
Q ss_pred ecCCCCCCCCCceeecCCcccccccccccc---CCcCcccCCc
Q 019740 12 CHSCNLPITDVEFSMSGNRPYHKHCYKEQH---HPKCDVCQNF 51 (336)
Q Consensus 12 C~~C~~~L~~~~F~~~dg~~yC~~CY~~~~---~pkC~~C~~~ 51 (336)
|..|...+........=|..||..|..+.+ ..+|..|+..
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 667777773322223357788888886433 3467777764
No 64
>PF02163 Peptidase_M50: Peptidase family M50; InterPro: IPR008915 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This entry contains metallopeptidases belonging to MEROPS peptidase family M50 (S2P protease family, clan MM). Members of the M50 metallopeptidase family include: mammalian sterol-regulatory element binding protein (SREBP) site 2 protease, Escherichia coli protease EcfE, stage IV sporulation protein FB and various hypothetical bacterial and eukaryotic homologues. A number of proteins are classified as non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity.; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 3B4R_A 3ID4_A 3ID2_A 2ZPL_B 3ID1_A 2ZPM_A 3ID3_B 2HGA_A.
Probab=47.85 E-value=14 Score=32.60 Aligned_cols=21 Identities=38% Similarity=0.298 Sum_probs=15.2
Q ss_pred hhhhhHHHHHHHHHHHhc-CCC
Q 019740 225 LTGSILAHEMMHAWLRLK-GYP 245 (336)
Q Consensus 225 ~~~~~lahe~~ha~l~~~-g~~ 245 (336)
+..+++.||++|++.... |.+
T Consensus 6 ~~i~i~~HE~gH~~~a~~~G~~ 27 (192)
T PF02163_consen 6 LLISIVLHELGHALAARLYGDK 27 (192)
T ss_dssp HHHHHHHHHHHHHHHHHTTT--
T ss_pred cccccccccccccccccccccc
Confidence 456899999999997653 543
No 65
>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=47.84 E-value=9.2 Score=32.03 Aligned_cols=11 Identities=45% Similarity=0.646 Sum_probs=9.7
Q ss_pred hhHHHHHHHHH
Q 019740 228 SILAHEMMHAW 238 (336)
Q Consensus 228 ~~lahe~~ha~ 238 (336)
.+++||+|||-
T Consensus 88 ~~~~HEigHaL 98 (140)
T smart00235 88 GVAAHELGHAL 98 (140)
T ss_pred ccHHHHHHHHh
Confidence 49999999994
No 66
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=47.47 E-value=19 Score=32.98 Aligned_cols=31 Identities=16% Similarity=0.323 Sum_probs=22.8
Q ss_pred CCeeecCCCCCCCCCceeecCCcccccccccc
Q 019740 8 ECFRCHSCNLPITDVEFSMSGNRPYHKHCYKE 39 (336)
Q Consensus 8 ~CF~C~~C~~~L~~~~F~~~dg~~yC~~CY~~ 39 (336)
+.|.|..|...+.+ .....=|..||..|-.+
T Consensus 17 ~~~~CpICld~~~d-PVvT~CGH~FC~~CI~~ 47 (193)
T PLN03208 17 GDFDCNICLDQVRD-PVVTLCGHLFCWPCIHK 47 (193)
T ss_pred CccCCccCCCcCCC-cEEcCCCchhHHHHHHH
Confidence 46889999887755 34445688999999854
No 67
>PF14247 DUF4344: Domain of unknown function (DUF4344)
Probab=47.45 E-value=26 Score=32.60 Aligned_cols=38 Identities=32% Similarity=0.254 Sum_probs=28.0
Q ss_pred hhhhHHHHHHHHHHHhcCCCCCCcchhhhHHHHHHHHhhh
Q 019740 226 TGSILAHEMMHAWLRLKGYPNLRPDVEEGICQVLAHMWLE 265 (336)
Q Consensus 226 ~~~~lahe~~ha~l~~~g~~~l~~~veeg~cq~~a~~wl~ 265 (336)
+-.||-||++||.+-+.+.|.|- -||--.-.+|-+.|-
T Consensus 92 ~~~~l~HE~GHAlI~~~~lPv~G--rEEDaaD~lAa~~ll 129 (220)
T PF14247_consen 92 VLFTLYHELGHALIDDLDLPVLG--REEDAADQLAALLLL 129 (220)
T ss_pred HHHHHHHHHHHHHHHHhcCCccc--chhhHHHHHHHHHHh
Confidence 45789999999999998777665 467766666555543
No 68
>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=47.34 E-value=12 Score=30.09 Aligned_cols=24 Identities=21% Similarity=0.483 Sum_probs=13.0
Q ss_pred CccccccccccccCCcCcccCCcccC
Q 019740 29 NRPYHKHCYKEQHHPKCDVCQNFIPT 54 (336)
Q Consensus 29 g~~yC~~CY~~~~~pkC~~C~~~I~~ 54 (336)
|.-||..|-.+ .-.|+-|++.|.+
T Consensus 58 g~~YCq~CAYk--kGiCamCGKki~d 81 (90)
T PF10235_consen 58 GAKYCQTCAYK--KGICAMCGKKILD 81 (90)
T ss_pred CCccChhhhcc--cCcccccCCeecc
Confidence 44566666433 2356666666643
No 69
>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=47.33 E-value=13 Score=32.99 Aligned_cols=24 Identities=33% Similarity=0.373 Sum_probs=17.1
Q ss_pred EEEEecCCChhhhhhhHHHHHHHHH
Q 019740 214 AILILYGLPRLLTGSILAHEMMHAW 238 (336)
Q Consensus 214 ~ilvl~glp~~~~~~~lahe~~ha~ 238 (336)
+|....+ +.+..+.++|||++|.+
T Consensus 122 ~v~~~~~-~~~~~~~~~aHElGH~l 145 (192)
T cd04267 122 GVVEDTG-FTLLTALTMAHELGHNL 145 (192)
T ss_pred EEEecCC-cceeehhhhhhhHHhhc
Confidence 3433333 36788899999999976
No 70
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=46.26 E-value=14 Score=34.72 Aligned_cols=42 Identities=17% Similarity=0.370 Sum_probs=31.0
Q ss_pred cCCCCCCCCCceee-cCCccccccccccccCCcCcccCCcccC
Q 019740 13 HSCNLPITDVEFSM-SGNRPYHKHCYKEQHHPKCDVCQNFIPT 54 (336)
Q Consensus 13 ~~C~~~L~~~~F~~-~dg~~yC~~CY~~~~~pkC~~C~~~I~~ 54 (336)
..|+..-....|+. .=..++|..|...-..+.|..|+++|..
T Consensus 7 n~C~~~~~~~~f~LTaC~HvfC~~C~k~~~~~~C~lCkk~ir~ 49 (233)
T KOG4739|consen 7 NKCFRFPSQDPFFLTACRHVFCEPCLKASSPDVCPLCKKSIRI 49 (233)
T ss_pred ccccccCCCCceeeeechhhhhhhhcccCCccccccccceeee
Confidence 34433333556665 5589999999998788899999999764
No 71
>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=46.24 E-value=11 Score=32.27 Aligned_cols=14 Identities=29% Similarity=0.268 Sum_probs=12.0
Q ss_pred hhhhhHHHHHHHHH
Q 019740 225 LTGSILAHEMMHAW 238 (336)
Q Consensus 225 ~~~~~lahe~~ha~ 238 (336)
..-.+++||++||-
T Consensus 93 ~~~~~~~HEiGHaL 106 (165)
T cd04268 93 RLRNTAEHELGHAL 106 (165)
T ss_pred HHHHHHHHHHHHHh
Confidence 45689999999996
No 72
>cd06158 S2P-M50_like_1 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group includes bacterial, eukaryotic, and Archaeal S2P/M50s homologs with a minimal core protein and no PDZ domains.
Probab=46.09 E-value=14 Score=32.99 Aligned_cols=18 Identities=28% Similarity=0.475 Sum_probs=14.4
Q ss_pred hhhhhHHHHHHHHHHHhc
Q 019740 225 LTGSILAHEMMHAWLRLK 242 (336)
Q Consensus 225 ~~~~~lahe~~ha~l~~~ 242 (336)
+.-|++.||++|||....
T Consensus 8 ~~~~i~~HE~aHa~~A~~ 25 (181)
T cd06158 8 VLLAITLHEFAHAYVAYR 25 (181)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 345899999999997664
No 73
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=45.97 E-value=5.5 Score=36.57 Aligned_cols=45 Identities=16% Similarity=0.352 Sum_probs=34.1
Q ss_pred eeecCCCCCCCCCceeecCCcccccccccccc--CCcCcccCCcccCC
Q 019740 10 FRCHSCNLPITDVEFSMSGNRPYHKHCYKEQH--HPKCDVCQNFIPTN 55 (336)
Q Consensus 10 F~C~~C~~~L~~~~F~~~dg~~yC~~CY~~~~--~pkC~~C~~~I~~~ 55 (336)
|.|..|++...+ .....-|..||..|+.+.+ ++.|.+|++...+.
T Consensus 197 F~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G~ 243 (259)
T COG5152 197 FLCGICKKDYES-PVVTECGHSFCSLCAIRKYQKGDECGVCGKATYGR 243 (259)
T ss_pred eeehhchhhccc-hhhhhcchhHHHHHHHHHhccCCcceecchhhccc
Confidence 789999887754 3444568889999987654 67899999877664
No 74
>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=45.77 E-value=12 Score=33.26 Aligned_cols=27 Identities=22% Similarity=0.245 Sum_probs=21.4
Q ss_pred EEEEEEecCCChhhhhhhHHHHHHHHH
Q 019740 212 VTAILILYGLPRLLTGSILAHEMMHAW 238 (336)
Q Consensus 212 v~~ilvl~glp~~~~~~~lahe~~ha~ 238 (336)
++-=+-|.-+|.-+.-.|++|||+|..
T Consensus 150 I~ln~~L~~~P~~~idYVvvHEL~Hl~ 176 (205)
T PF01863_consen 150 ITLNWRLVMAPPEVIDYVVVHELCHLR 176 (205)
T ss_pred EEeecccccCCccHHHHHHHHHHHHhc
Confidence 333345666999999999999999974
No 75
>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=45.73 E-value=15 Score=38.96 Aligned_cols=40 Identities=20% Similarity=0.222 Sum_probs=28.2
Q ss_pred hhhHHHHHHHHHHHhc-CCCCC-CcchhhhHHHHHHHHhhhc
Q 019740 227 GSILAHEMMHAWLRLK-GYPNL-RPDVEEGICQVLAHMWLES 266 (336)
Q Consensus 227 ~~~lahe~~ha~l~~~-g~~~l-~~~veeg~cq~~a~~wl~~ 266 (336)
..++|||++|-|.--- .-..= +..+-||++-.+.+.+++.
T Consensus 280 ~~viaHElAHqWfGNlVT~~~W~d~WLnEGfaty~e~~~~~~ 321 (601)
T TIGR02411 280 VDVIAHELAHSWSGNLVTNCSWEHFWLNEGWTVYLERRIVGR 321 (601)
T ss_pred hhhHHHHHHhhccCceeecCCchHHHHHhhHHHHHHHHHHHH
Confidence 3699999999997421 11111 3578999999998877653
No 76
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=45.59 E-value=13 Score=31.92 Aligned_cols=24 Identities=25% Similarity=0.549 Sum_probs=19.4
Q ss_pred cCCCCccCCCCCceEEcCCCceeccchhhhc
Q 019740 84 CCSCERMEPRDTKYLSLDDGRKLCLECLDSA 114 (336)
Q Consensus 84 C~~C~~~l~~~~~f~~~~dG~~yC~~C~~~~ 114 (336)
|..|+.+| |. .||..||+.|-.+.
T Consensus 31 Cp~Cg~PL------F~-KdG~v~CPvC~~~~ 54 (131)
T COG1645 31 CPKCGTPL------FR-KDGEVFCPVCGYRE 54 (131)
T ss_pred CcccCCcc------ee-eCCeEECCCCCceE
Confidence 88899998 34 49999999997544
No 77
>PRK04860 hypothetical protein; Provisional
Probab=45.48 E-value=15 Score=32.41 Aligned_cols=27 Identities=19% Similarity=0.380 Sum_probs=20.8
Q ss_pred ChhhhhhhHHHHHHHHHHHhc-C--CCCCCc
Q 019740 222 PRLLTGSILAHEMMHAWLRLK-G--YPNLRP 249 (336)
Q Consensus 222 p~~~~~~~lahe~~ha~l~~~-g--~~~l~~ 249 (336)
+.-.+-.|++|||+|.++.+. | +|. +.
T Consensus 59 ~~~~l~~~v~HEl~H~~~~~~~g~~~~H-g~ 88 (160)
T PRK04860 59 QQAFIDEVVPHELAHLLVYQLFGRVAPH-GK 88 (160)
T ss_pred cHHHHHhHHHHHHHHHHHHHHcCCCCCC-CH
Confidence 455667899999999999976 4 555 44
No 78
>KOG1420 consensus Ca2+-activated K+ channel Slowpoke, alpha subunit [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=44.45 E-value=27 Score=37.11 Aligned_cols=6 Identities=17% Similarity=0.224 Sum_probs=2.4
Q ss_pred HHHHhh
Q 019740 311 GKFFKH 316 (336)
Q Consensus 311 ~~~~~~ 316 (336)
-.|+..
T Consensus 50 w~fl~s 55 (1103)
T KOG1420|consen 50 WAFLAS 55 (1103)
T ss_pred HHHHHH
Confidence 344443
No 79
>KOG2130 consensus Phosphatidylserine-specific receptor PtdSerR, contains JmjC domain [Chromatin structure and dynamics; Signal transduction mechanisms]
Probab=43.94 E-value=23 Score=34.90 Aligned_cols=12 Identities=25% Similarity=0.415 Sum_probs=7.0
Q ss_pred cHHHHHHhhcCc
Q 019740 149 ERQALNEAMEGE 160 (336)
Q Consensus 149 ~~~ALn~a~~~e 160 (336)
.-+|-|..+.+.
T Consensus 200 gTSAWNtll~Gh 211 (407)
T KOG2130|consen 200 GTSAWNTLLQGH 211 (407)
T ss_pred chHHHHHHhhcc
Confidence 356667766443
No 80
>PF00413 Peptidase_M10: Matrixin This Prosite motif covers only the active site.; InterPro: IPR001818 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M10 (clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. Sequences having this domain are extracellular metalloproteases, such as collagenase and stromelysin, which degrade the extracellular matrix, are known as matrixins. They are zinc-dependent, calcium-activated proteases synthesised as inactive precursors (zymogens), which are proteolytically cleaved to yield the active enzyme [, ]. All matrixins and related proteins possess 2 domains: an N-terminal domain, and a zinc-binding active site domain. The N-terminal domain peptide, cleaved during the activation step, includes a conserved PRCGVPDV octapeptide, known as the cysteine switch, whose Cys residue chelates the active site zinc atom, rendering the enzyme inactive [, ]. The active enzyme degrades components of the extracellular matrix, playing a role in the initial steps of tissue remodelling during morphogenesis, wound healing, angiogenesis and tumour invasion [, ].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis, 0031012 extracellular matrix; PDB: 1Q3A_C 3V96_B 1HV5_D 1CXV_A 1SRP_A 1FBL_A 1ZVX_A 1JH1_A 1I76_A 2OY4_A ....
Probab=43.58 E-value=13 Score=31.26 Aligned_cols=18 Identities=28% Similarity=0.108 Sum_probs=13.9
Q ss_pred CChhhhhhhHHHHHHHHH
Q 019740 221 LPRLLTGSILAHEMMHAW 238 (336)
Q Consensus 221 lp~~~~~~~lahe~~ha~ 238 (336)
.+......++.||++||-
T Consensus 100 ~~~~~~~~v~~HEiGHaL 117 (154)
T PF00413_consen 100 DSGNDLQSVAIHEIGHAL 117 (154)
T ss_dssp SSSEEHHHHHHHHHHHHT
T ss_pred hhhhhhhhhhhhcccccc
Confidence 344556789999999994
No 81
>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=42.31 E-value=30 Score=36.25 Aligned_cols=45 Identities=22% Similarity=0.187 Sum_probs=28.8
Q ss_pred hhhhhhHHHHHHHHH---HHhcC----CCCCCcchhh---hHHHHHHHHhhhccc
Q 019740 224 LLTGSILAHEMMHAW---LRLKG----YPNLRPDVEE---GICQVLAHMWLESEI 268 (336)
Q Consensus 224 ~~~~~~lahe~~ha~---l~~~g----~~~l~~~vee---g~cq~~a~~wl~~~~ 268 (336)
.---.+||||++||+ +--++ +...+.++-| =+++.+.+-||....
T Consensus 335 ~~dv~TL~HElGHa~H~~~s~~~~~~~~~~~~~~~aE~aS~~~E~l~~~~l~~~~ 389 (549)
T TIGR02289 335 SGDIDVLTHEAGHAFHVYESRKDLLPEYRWPTYEAAELASMSMELLSMPWWDLFY 389 (549)
T ss_pred hhHHHHHHHHhhHHHHHHHhcCCcccccccCcchhhhhhHHHHHHHHHHHHHHHc
Confidence 344578999999997 32222 3333445555 678888888876543
No 82
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=41.80 E-value=25 Score=37.82 Aligned_cols=22 Identities=23% Similarity=0.520 Sum_probs=11.8
Q ss_pred ccCCCCccCCCCCceEEcCCCceeccchhhh
Q 019740 83 RCCSCERMEPRDTKYLSLDDGRKLCLECLDS 113 (336)
Q Consensus 83 ~C~~C~~~l~~~~~f~~~~dG~~yC~~C~~~ 113 (336)
.|..|+..++ .+..+|.+|-.+
T Consensus 29 ~Cp~CG~~~~---------~~~~fC~~CG~~ 50 (645)
T PRK14559 29 PCPQCGTEVP---------VDEAHCPNCGAE 50 (645)
T ss_pred cCCCCCCCCC---------cccccccccCCc
Confidence 3666666554 233446666544
No 83
>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=41.62 E-value=19 Score=30.63 Aligned_cols=16 Identities=31% Similarity=0.329 Sum_probs=13.7
Q ss_pred hhhhhhhHHHHHHHHH
Q 019740 223 RLLTGSILAHEMMHAW 238 (336)
Q Consensus 223 ~~~~~~~lahe~~ha~ 238 (336)
...+..+++||++|+.
T Consensus 93 ~~~~~~~~~HElGH~L 108 (167)
T cd00203 93 TKEGAQTIAHELGHAL 108 (167)
T ss_pred cccchhhHHHHHHHHh
Confidence 3477899999999997
No 84
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=41.34 E-value=11 Score=29.61 Aligned_cols=29 Identities=28% Similarity=0.668 Sum_probs=21.0
Q ss_pred eecCCCCCCCCCcee--ecC---Ccccccccccc
Q 019740 11 RCHSCNLPITDVEFS--MSG---NRPYHKHCYKE 39 (336)
Q Consensus 11 ~C~~C~~~L~~~~F~--~~d---g~~yC~~CY~~ 39 (336)
.|..|+.||.....+ +.| +.-||.-||..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 489999999875532 233 35799999975
No 85
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=41.28 E-value=9.9 Score=28.22 Aligned_cols=15 Identities=27% Similarity=0.428 Sum_probs=6.8
Q ss_pred ccCCCCccCCCCCce
Q 019740 83 RCCSCERMEPRDTKY 97 (336)
Q Consensus 83 ~C~~C~~~l~~~~~f 97 (336)
.|.+|+..|..++.+
T Consensus 11 ~CtSCg~~i~p~e~~ 25 (61)
T COG2888 11 VCTSCGREIAPGETA 25 (61)
T ss_pred eeccCCCEeccCCce
Confidence 455555554334433
No 86
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=40.75 E-value=5.3 Score=36.16 Aligned_cols=51 Identities=16% Similarity=0.280 Sum_probs=39.3
Q ss_pred cCCCCCccCCCCccCCCCCceEEcCCCceeccchhhhcccCCCCCCchhhHH
Q 019740 77 ERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEI 128 (336)
Q Consensus 77 ~H~~CF~C~~C~~~l~~~~~f~~~~dG~~yC~~C~~~~v~~~~~C~~c~~~I 128 (336)
||..|..|..|...+......+.. +|..||...+.........|..|...|
T Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~ 69 (235)
T KOG0490|consen 19 WHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTI 69 (235)
T ss_pred HHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCc
Confidence 399999999999998544556666 999999999886334566777777665
No 87
>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=40.60 E-value=15 Score=32.50 Aligned_cols=18 Identities=28% Similarity=0.318 Sum_probs=14.2
Q ss_pred CChhhhhhhHHHHHHHHH
Q 019740 221 LPRLLTGSILAHEMMHAW 238 (336)
Q Consensus 221 lp~~~~~~~lahe~~ha~ 238 (336)
.|......++|||++|.+
T Consensus 137 ~~~~~~~~~~AHEiGH~l 154 (196)
T PF13688_consen 137 PPTYNGAITFAHEIGHNL 154 (196)
T ss_dssp --HHHHHHHHHHHHHHHT
T ss_pred CCCCceehhhHHhHHHhc
Confidence 446777899999999987
No 88
>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=40.58 E-value=19 Score=28.02 Aligned_cols=25 Identities=24% Similarity=0.218 Sum_probs=18.9
Q ss_pred hhhhhhhHHHHHHHHHHHhcCCCCCC
Q 019740 223 RLLTGSILAHEMMHAWLRLKGYPNLR 248 (336)
Q Consensus 223 ~~~~~~~lahe~~ha~l~~~g~~~l~ 248 (336)
+|=||-|+|||+.+-|=+ .|++--|
T Consensus 49 MLGFGEl~AhE~~fr~gW-~g~ki~P 73 (77)
T PF08219_consen 49 MLGFGELFAHEIAFRLGW-SGTKIFP 73 (77)
T ss_pred hHhHHHHHHHHHHHHhcc-CcceecC
Confidence 688999999999887744 4665433
No 89
>PRK00420 hypothetical protein; Validated
Probab=40.49 E-value=20 Score=29.98 Aligned_cols=26 Identities=23% Similarity=0.369 Sum_probs=19.6
Q ss_pred ccCCCCccCCCCCceEEcCCCceeccchhhhc
Q 019740 83 RCCSCERMEPRDTKYLSLDDGRKLCLECLDSA 114 (336)
Q Consensus 83 ~C~~C~~~l~~~~~f~~~~dG~~yC~~C~~~~ 114 (336)
.|..|+.+| +.+.+|+.+|+.|-...
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 477788776 34459999999997754
No 90
>PRK14873 primosome assembly protein PriA; Provisional
Probab=40.36 E-value=23 Score=38.27 Aligned_cols=52 Identities=8% Similarity=0.057 Sum_probs=26.7
Q ss_pred cccccCCCcccccccccccccccceeEE-EEEEecCCCh-hhhhhhHHHHHHHHH
Q 019740 186 RRPRIGAGYRLIDMITEPYRLIRRCEVT-AILILYGLPR-LLTGSILAHEMMHAW 238 (336)
Q Consensus 186 ~~~r~~~~~~~~~~~t~~~~~~~~~~v~-~ilvl~glp~-~~~~~~lahe~~ha~ 238 (336)
..|-.+.+-+..++.++...+.++.+-- .++|. +-|. .+..+.+.|.+--.|
T Consensus 502 ~~pDfRA~Er~~qll~qvagragr~~~~G~V~iq-~~p~~~~~~~l~~~d~~~F~ 555 (665)
T PRK14873 502 GRQDLRAAEDTLRRWMAAAALVRPRADGGQVVVV-AESSLPTVQALIRWDPVGHA 555 (665)
T ss_pred cCCCcChHHHHHHHHHHHHHhhcCCCCCCEEEEE-eCCCCHHHHHHHhCCHHHHH
Confidence 3444455555555555554444332211 23333 4665 455667777776666
No 91
>PF05299 Peptidase_M61: M61 glycyl aminopeptidase; InterPro: IPR007963 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 M61 (glycyl aminopeptidase family, clan MA(E)).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 is glycyl aminopeptidase from Sphingomonas capsulata.
Probab=39.46 E-value=15 Score=31.02 Aligned_cols=41 Identities=29% Similarity=0.493 Sum_probs=29.2
Q ss_pred hhhhHHHHHHHHHH--HhcC--C-------CCCC--cchhhhHHHHHHHHhhhc
Q 019740 226 TGSILAHEMMHAWL--RLKG--Y-------PNLR--PDVEEGICQVLAHMWLES 266 (336)
Q Consensus 226 ~~~~lahe~~ha~l--~~~g--~-------~~l~--~~veeg~cq~~a~~wl~~ 266 (336)
+-.++|||+-|+|- |+.. . |+.+ +-|-||+=+.++.+-|-+
T Consensus 4 ~l~l~sHEffH~WnvkrirP~~l~p~dy~~~~~t~~LWv~EG~T~Y~~~l~l~R 57 (122)
T PF05299_consen 4 FLGLLSHEFFHSWNVKRIRPAELGPFDYEKPNYTELLWVYEGFTSYYGDLLLVR 57 (122)
T ss_pred hhhhhhhhccccccceEeccccccCCCCCCCCCCCCEeeeeCcHHHHHHHHHHH
Confidence 45789999999994 4432 1 1222 468899999998887655
No 92
>PRK02870 heat shock protein HtpX; Provisional
Probab=39.36 E-value=24 Score=34.87 Aligned_cols=24 Identities=33% Similarity=0.461 Sum_probs=17.9
Q ss_pred EEEEecC----CChhhhhhhHHHHHHHH
Q 019740 214 AILILYG----LPRLLTGSILAHEMMHA 237 (336)
Q Consensus 214 ~ilvl~g----lp~~~~~~~lahe~~ha 237 (336)
.|.|-.| |++--..+|||||++|.
T Consensus 157 ~Ivvt~GLL~~L~~dEL~aVlAHELgHi 184 (336)
T PRK02870 157 MVAITTGLLEKLDRDELQAVMAHELSHI 184 (336)
T ss_pred EEEEehHHhhhCCHHHHHHHHHHHHHHH
Confidence 3445445 56667789999999997
No 93
>KOG3714 consensus Meprin A metalloprotease [Posttranslational modification, protein turnover, chaperones]
Probab=39.30 E-value=14 Score=37.45 Aligned_cols=11 Identities=45% Similarity=0.821 Sum_probs=9.7
Q ss_pred hhHHHHHHHHH
Q 019740 228 SILAHEMMHAW 238 (336)
Q Consensus 228 ~~lahe~~ha~ 238 (336)
.|++||||||=
T Consensus 161 G~i~HEl~HaL 171 (411)
T KOG3714|consen 161 GTIVHELMHAL 171 (411)
T ss_pred chhHHHHHHHh
Confidence 57899999995
No 94
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=38.88 E-value=38 Score=39.10 Aligned_cols=14 Identities=36% Similarity=0.318 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHhcC
Q 019740 230 LAHEMMHAWLRLKG 243 (336)
Q Consensus 230 lahe~~ha~l~~~g 243 (336)
.||.+-||=.|-|=
T Consensus 906 YAHPyFHAAKRRNC 919 (1337)
T PRK14714 906 YAHPYFHAAKRRNC 919 (1337)
T ss_pred cccchhhhHhhcCC
Confidence 58999999888763
No 95
>KOG3624 consensus M13 family peptidase [Amino acid transport and metabolism]
Probab=38.75 E-value=14 Score=39.76 Aligned_cols=15 Identities=27% Similarity=0.514 Sum_probs=13.2
Q ss_pred hhhhhHHHHHHHHHH
Q 019740 225 LTGSILAHEMMHAWL 239 (336)
Q Consensus 225 ~~~~~lahe~~ha~l 239 (336)
..|.+|||||+|+|=
T Consensus 517 ~iG~vigHEl~H~FD 531 (687)
T KOG3624|consen 517 GIGFVIGHELTHGFD 531 (687)
T ss_pred HHHHHHHHHHhhccc
Confidence 479999999999983
No 96
>PRK04897 heat shock protein HtpX; Provisional
Probab=38.60 E-value=13 Score=35.88 Aligned_cols=19 Identities=21% Similarity=0.274 Sum_probs=15.9
Q ss_pred CCChhhhhhhHHHHHHHHH
Q 019740 220 GLPRLLTGSILAHEMMHAW 238 (336)
Q Consensus 220 glp~~~~~~~lahe~~ha~ 238 (336)
.|++--..+|||||++|.-
T Consensus 131 ~l~~~El~aVlAHElgHi~ 149 (298)
T PRK04897 131 IMNREELEGVIGHEISHIR 149 (298)
T ss_pred hCCHHHHHHHHHHHHHHHh
Confidence 4677778999999999954
No 97
>KOG3931 consensus Uncharacterized conserved protein [Function unknown]
Probab=38.38 E-value=17 Score=36.28 Aligned_cols=24 Identities=38% Similarity=0.375 Sum_probs=19.7
Q ss_pred cCCChhhhhhhHHHHHHHHHHHhc
Q 019740 219 YGLPRLLTGSILAHEMMHAWLRLK 242 (336)
Q Consensus 219 ~glp~~~~~~~lahe~~ha~l~~~ 242 (336)
.=-||--.--.|-|||.||||...
T Consensus 98 kLRPRkDLVETLLHEMIHAYlFV~ 121 (484)
T KOG3931|consen 98 KLRPRKDLVETLLHEMIHAYLFVT 121 (484)
T ss_pred ccCchHHHHHHHHHHHHHHheeEe
Confidence 334777778899999999999884
No 98
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=37.95 E-value=16 Score=35.84 Aligned_cols=44 Identities=16% Similarity=0.501 Sum_probs=29.6
Q ss_pred eecCCCCCCCCCceeecCCccccccccccccCCcCcccCCcccC
Q 019740 11 RCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPT 54 (336)
Q Consensus 11 ~C~~C~~~L~~~~F~~~dg~~yC~~CY~~~~~pkC~~C~~~I~~ 54 (336)
.|..|+.+|.-..-..--..+||-+|-..---..|..|..+|.-
T Consensus 92 fCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~dK~Cp~C~d~Vqr 135 (389)
T KOG2932|consen 92 FCDRCDFPIAIYGRMIPCKHVFCLECARSDSDKICPLCDDRVQR 135 (389)
T ss_pred eecccCCcceeeecccccchhhhhhhhhcCccccCcCcccHHHH
Confidence 47888888865444444567788888765445578888877653
No 99
>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=37.77 E-value=21 Score=34.47 Aligned_cols=17 Identities=35% Similarity=0.239 Sum_probs=14.9
Q ss_pred hhhhhHHHHHHHHHHHh
Q 019740 225 LTGSILAHEMMHAWLRL 241 (336)
Q Consensus 225 ~~~~~lahe~~ha~l~~ 241 (336)
+..+++.||++||+...
T Consensus 134 l~isvvvHElgHal~A~ 150 (277)
T cd06162 134 LLISGVVHEMGHGVAAV 150 (277)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 57799999999999766
No 100
>COG1451 Predicted metal-dependent hydrolase [General function prediction only]
Probab=37.64 E-value=16 Score=33.96 Aligned_cols=27 Identities=19% Similarity=0.193 Sum_probs=21.6
Q ss_pred EEEEEEecCCChhhhhhhHHHHHHHHH
Q 019740 212 VTAILILYGLPRLLTGSILAHEMMHAW 238 (336)
Q Consensus 212 v~~ilvl~glp~~~~~~~lahe~~ha~ 238 (336)
++==+.|-.+|.-+...|++||++|--
T Consensus 161 i~~~~~l~~~p~~~i~YVvvHELaHLk 187 (223)
T COG1451 161 IRFNWRLVMAPEEVIDYVVVHELAHLK 187 (223)
T ss_pred EEeehhhhcCCHHHHHHHHHHHHHHHh
Confidence 333346778999999999999999953
No 101
>PRK00420 hypothetical protein; Validated
Probab=37.44 E-value=20 Score=29.98 Aligned_cols=23 Identities=22% Similarity=0.511 Sum_probs=13.4
Q ss_pred eecCCCCCCCCCceeecCCcccccccc
Q 019740 11 RCHSCNLPITDVEFSMSGNRPYHKHCY 37 (336)
Q Consensus 11 ~C~~C~~~L~~~~F~~~dg~~yC~~CY 37 (336)
.|..|+.|| |-.++|+.||..|-
T Consensus 25 ~CP~Cg~pL----f~lk~g~~~Cp~Cg 47 (112)
T PRK00420 25 HCPVCGLPL----FELKDGEVVCPVHG 47 (112)
T ss_pred CCCCCCCcc----eecCCCceECCCCC
Confidence 466777666 22266766665553
No 102
>PRK11827 hypothetical protein; Provisional
Probab=37.34 E-value=25 Score=26.15 Aligned_cols=15 Identities=20% Similarity=0.485 Sum_probs=12.0
Q ss_pred ceeccccccchhcHH
Q 019740 137 MKVEQQVPLLLVERQ 151 (336)
Q Consensus 137 ~~i~~~~p~~lV~~~ 151 (336)
.||.+.+|++|++-.
T Consensus 36 YPI~dgIPVlL~deA 50 (60)
T PRK11827 36 FPLRDGIPVLLETEA 50 (60)
T ss_pred ccccCCccccCHHHh
Confidence 588899999987643
No 103
>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=37.12 E-value=20 Score=31.71 Aligned_cols=13 Identities=31% Similarity=0.327 Sum_probs=11.4
Q ss_pred hhhhHHHHHHHHH
Q 019740 226 TGSILAHEMMHAW 238 (336)
Q Consensus 226 ~~~~lahe~~ha~ 238 (336)
.-.++|||+.|.+
T Consensus 111 ~~~~~aHElGH~l 123 (173)
T PF13574_consen 111 GIDTFAHELGHQL 123 (173)
T ss_dssp HHHHHHHHHHHHH
T ss_pred eeeeehhhhHhhc
Confidence 5568999999998
No 104
>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=36.91 E-value=23 Score=33.83 Aligned_cols=28 Identities=29% Similarity=0.483 Sum_probs=19.6
Q ss_pred EecCCChhhhhhhHHHHHHHHHHHhc-CCC
Q 019740 217 ILYGLPRLLTGSILAHEMMHAWLRLK-GYP 245 (336)
Q Consensus 217 vl~glp~~~~~~~lahe~~ha~l~~~-g~~ 245 (336)
+++++. .+.-+++.||++||+.... |.+
T Consensus 110 ~~~~~i-aL~isv~iHElgHa~~Ar~~G~~ 138 (263)
T cd06159 110 LPYGII-ALVVGVVVHELSHGILARVEGIK 138 (263)
T ss_pred HHHHHH-HHHHHHHHHHHHHHHHHHHcCCE
Confidence 334442 3577899999999997663 654
No 105
>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=36.82 E-value=26 Score=31.87 Aligned_cols=22 Identities=41% Similarity=0.498 Sum_probs=17.4
Q ss_pred hhhhhhHHHHHHHHHHHhc-CCC
Q 019740 224 LLTGSILAHEMMHAWLRLK-GYP 245 (336)
Q Consensus 224 ~~~~~~lahe~~ha~l~~~-g~~ 245 (336)
.++.+++.||+.|++.... |.+
T Consensus 36 ~l~~~v~iHElgH~~~A~~~G~~ 58 (208)
T cd06161 36 LLFLSVLLHELGHALVARRYGIR 58 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCC
Confidence 5778999999999996553 654
No 106
>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=35.88 E-value=21 Score=33.31 Aligned_cols=29 Identities=31% Similarity=0.439 Sum_probs=23.1
Q ss_pred cCCChhhhhhhHHHHHHHHHHHhcCCCCC
Q 019740 219 YGLPRLLTGSILAHEMMHAWLRLKGYPNL 247 (336)
Q Consensus 219 ~glp~~~~~~~lahe~~ha~l~~~g~~~l 247 (336)
|+=.-+..-+|.|||.+||-..-+||.-|
T Consensus 82 y~~~SiaAvaVAAHEvGHAiQ~a~~Y~pl 110 (222)
T PF04298_consen 82 YNGRSIAAVAVAAHEVGHAIQHAEGYAPL 110 (222)
T ss_pred CCCCCHHHHHHHHHHHhHHHhccccCcHH
Confidence 44455677799999999999999998644
No 107
>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=35.69 E-value=19 Score=30.82 Aligned_cols=16 Identities=31% Similarity=0.223 Sum_probs=13.3
Q ss_pred hhhhhhhHHHHHHHHH
Q 019740 223 RLLTGSILAHEMMHAW 238 (336)
Q Consensus 223 ~~~~~~~lahe~~ha~ 238 (336)
...+-+++.||++||-
T Consensus 101 ~~~~~~~~~HEiGHaL 116 (156)
T cd04279 101 AENLQAIALHELGHAL 116 (156)
T ss_pred chHHHHHHHHHhhhhh
Confidence 4567799999999985
No 108
>PRK00807 50S ribosomal protein L24e; Validated
Probab=35.62 E-value=11 Score=27.16 Aligned_cols=35 Identities=14% Similarity=0.334 Sum_probs=21.5
Q ss_pred cCcccCCcccCCCC-ceEEEeeecccccccCCCCcCCCCCccCCCCccC
Q 019740 44 KCDVCQNFIPTNSA-GLIEYRAHPFWLQKYCPSHERDGTPRCCSCERME 91 (336)
Q Consensus 44 kC~~C~~~I~~~~~-g~i~~~~~~fW~qkyCp~H~H~~CF~C~~C~~~l 91 (336)
.|..|+..|.+..+ .++...++.|+ |.+..|.+.+
T Consensus 3 ~C~fcG~~I~pg~G~~~vr~Dgkv~~-------------Fcs~KC~~~f 38 (52)
T PRK00807 3 TCSFCGKEIEPGTGKMYVKKDGTILY-------------FCSSKCEKNY 38 (52)
T ss_pred ccCCCCCeEcCCCCeEEEEeCCcEEE-------------EeCHHHHHHH
Confidence 68888888884432 22455566662 5555776644
No 109
>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=35.29 E-value=34 Score=23.15 Aligned_cols=31 Identities=32% Similarity=0.706 Sum_probs=19.9
Q ss_pred ccCCCCccCCCCCceEEcCCCceeccchhhh
Q 019740 83 RCCSCERMEPRDTKYLSLDDGRKLCLECLDS 113 (336)
Q Consensus 83 ~C~~C~~~l~~~~~f~~~~dG~~yC~~C~~~ 113 (336)
+|+-|+++.......+.-.++-..|..|...
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~ 33 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECVEQ 33 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHHHH
Confidence 5889999987556666554477889999765
No 110
>PRK03001 M48 family peptidase; Provisional
Probab=35.04 E-value=18 Score=34.48 Aligned_cols=18 Identities=28% Similarity=0.394 Sum_probs=14.9
Q ss_pred CChhhhhhhHHHHHHHHH
Q 019740 221 LPRLLTGSILAHEMMHAW 238 (336)
Q Consensus 221 lp~~~~~~~lahe~~ha~ 238 (336)
|..--..+|||||++|.-
T Consensus 119 l~~~El~aVlAHElgHi~ 136 (283)
T PRK03001 119 LSEREIRGVMAHELAHVK 136 (283)
T ss_pred CCHHHHHHHHHHHHHHHh
Confidence 566667899999999975
No 111
>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=34.77 E-value=27 Score=32.37 Aligned_cols=22 Identities=41% Similarity=0.680 Sum_probs=17.4
Q ss_pred hhhhhhHHHHHHHHHHHhc-CCC
Q 019740 224 LLTGSILAHEMMHAWLRLK-GYP 245 (336)
Q Consensus 224 ~~~~~~lahe~~ha~l~~~-g~~ 245 (336)
.++.+++.||++|++.... |++
T Consensus 51 ~l~~~v~iHElgH~~~A~~~G~~ 73 (227)
T cd06164 51 LLFASVLLHELGHSLVARRYGIP 73 (227)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCe
Confidence 4788999999999995543 654
No 112
>PRK14015 pepN aminopeptidase N; Provisional
Probab=34.70 E-value=37 Score=37.87 Aligned_cols=41 Identities=20% Similarity=0.399 Sum_probs=27.5
Q ss_pred hhhhHHHHHHHHHHHhc-CCCCC-CcchhhhHHHHHHHHhhhc
Q 019740 226 TGSILAHEMMHAWLRLK-GYPNL-RPDVEEGICQVLAHMWLES 266 (336)
Q Consensus 226 ~~~~lahe~~ha~l~~~-g~~~l-~~~veeg~cq~~a~~wl~~ 266 (336)
..+++|||+.|-|.-=. -.+.- +..+-||+.-.+...|.+.
T Consensus 296 i~~vIaHElaHqWFGNlVT~~~W~dLWLnEGFAty~e~~~~~~ 338 (875)
T PRK14015 296 IESVIAHEYFHNWTGNRVTCRDWFQLSLKEGLTVFRDQEFSAD 338 (875)
T ss_pred HHHHHHHHHHHHHHhCcceecchhhhhhhhHHHHHHHHHHHHH
Confidence 45899999999995210 00111 2457999999988887654
No 113
>PRK03072 heat shock protein HtpX; Provisional
Probab=34.62 E-value=18 Score=34.83 Aligned_cols=20 Identities=25% Similarity=0.321 Sum_probs=16.0
Q ss_pred cCCChhhhhhhHHHHHHHHH
Q 019740 219 YGLPRLLTGSILAHEMMHAW 238 (336)
Q Consensus 219 ~glp~~~~~~~lahe~~ha~ 238 (336)
.-|.+--..+|+|||+.|.-
T Consensus 120 ~~l~~~El~aVlAHElgHi~ 139 (288)
T PRK03072 120 QILNERELRGVLGHELSHVY 139 (288)
T ss_pred HhCCHHHHHHHHHHHHHHHh
Confidence 34677777899999999964
No 114
>PRK05457 heat shock protein HtpX; Provisional
Probab=34.46 E-value=19 Score=34.65 Aligned_cols=19 Identities=32% Similarity=0.415 Sum_probs=16.3
Q ss_pred CCChhhhhhhHHHHHHHHH
Q 019740 220 GLPRLLTGSILAHEMMHAW 238 (336)
Q Consensus 220 glp~~~~~~~lahe~~ha~ 238 (336)
.|++--..+|+|||+.|.-
T Consensus 128 ~L~~~El~aVlAHElgHi~ 146 (284)
T PRK05457 128 NMSRDEVEAVLAHEISHIA 146 (284)
T ss_pred hCCHHHHHHHHHHHHHHHH
Confidence 4788888999999999963
No 115
>PHA03309 transcriptional regulator ICP4; Provisional
Probab=34.38 E-value=31 Score=38.34 Aligned_cols=15 Identities=33% Similarity=0.563 Sum_probs=8.0
Q ss_pred cccccchhcHHHHHH
Q 019740 141 QQVPLLLVERQALNE 155 (336)
Q Consensus 141 ~~~p~~lV~~~ALn~ 155 (336)
+.+|+.+.....|.+
T Consensus 1494 qdvplpfltaatlrk 1508 (2033)
T PHA03309 1494 QDVPLPFLTAATLRK 1508 (2033)
T ss_pred CCCCchhhhHHHHHH
Confidence 455655555555544
No 116
>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=34.24 E-value=32 Score=30.88 Aligned_cols=17 Identities=24% Similarity=0.296 Sum_probs=12.3
Q ss_pred ChhhhhhhHHHHHHHHH
Q 019740 222 PRLLTGSILAHEMMHAW 238 (336)
Q Consensus 222 p~~~~~~~lahe~~ha~ 238 (336)
+.-....+++||+|||-
T Consensus 75 ~~c~~~~~i~HEl~HaL 91 (191)
T PF01400_consen 75 DGCFSVGTILHELGHAL 91 (191)
T ss_dssp TTC-SHHHHHHHHHHHH
T ss_pred ceeCCccchHHHHHHHH
Confidence 33345578999999996
No 117
>PF10463 Peptidase_U49: Peptidase U49; InterPro: IPR019504 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This entry contains peptidases belonging to MEROPS peptidase family U49 (Lit peptidase, clan U-). The Lit peptidase from Escherichia coli functions in bacterial cell death in response to infection by Enterobacteria phage T4. Following binding of Gol peptide to domains II and III of elongation factor Tu, the Lit peptidase cleaves domain I of the elongation factor. This prevents binding of guanine nucleotides, shuts down translation and leads to cell death.
Probab=34.19 E-value=44 Score=30.81 Aligned_cols=48 Identities=25% Similarity=0.178 Sum_probs=36.3
Q ss_pred CChhhhhhhHHHHHHHHHHHhcCC-CCCCcchhhhHHHHHHHHhhhccc
Q 019740 221 LPRLLTGSILAHEMMHAWLRLKGY-PNLRPDVEEGICQVLAHMWLESEI 268 (336)
Q Consensus 221 lp~~~~~~~lahe~~ha~l~~~g~-~~l~~~veeg~cq~~a~~wl~~~~ 268 (336)
|=-...+=+|+||+.|+.+.-.+. ..-...-||==|-..|-.||-+..
T Consensus 96 l~~~A~~fil~HE~~Hv~~~h~~~~~~~~~~~eE~~AD~~A~~~il~~~ 144 (206)
T PF10463_consen 96 LFCCAIAFILLHELAHVVLGHEGDSSPSQSIQEEKEADSYATEMILSDV 144 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHcCccccccchhHHHHHhhhHHHHHHHHHHH
Confidence 334567789999999988887776 444466677789999999975543
No 118
>PRK03982 heat shock protein HtpX; Provisional
Probab=34.17 E-value=20 Score=34.33 Aligned_cols=18 Identities=28% Similarity=0.313 Sum_probs=15.2
Q ss_pred CChhhhhhhHHHHHHHHH
Q 019740 221 LPRLLTGSILAHEMMHAW 238 (336)
Q Consensus 221 lp~~~~~~~lahe~~ha~ 238 (336)
|..--.-+|||||++|.-
T Consensus 120 l~~~El~AVlAHElgHi~ 137 (288)
T PRK03982 120 LNEDELEGVIAHELTHIK 137 (288)
T ss_pred CCHHHHHHHHHHHHHHHH
Confidence 566678899999999975
No 119
>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=34.10 E-value=21 Score=32.70 Aligned_cols=11 Identities=36% Similarity=0.591 Sum_probs=9.8
Q ss_pred hhHHHHHHHHH
Q 019740 228 SILAHEMMHAW 238 (336)
Q Consensus 228 ~~lahe~~ha~ 238 (336)
.+++||||||-
T Consensus 89 Gti~HEl~HaL 99 (200)
T cd04281 89 GIVVHELGHVI 99 (200)
T ss_pred chHHHHHHHHh
Confidence 58999999995
No 120
>PF06037 DUF922: Bacterial protein of unknown function (DUF922); InterPro: IPR010321 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=33.79 E-value=64 Score=28.44 Aligned_cols=30 Identities=27% Similarity=0.434 Sum_probs=23.7
Q ss_pred EEEEEecCCChhh----------------hhhhHHHHHHHHHHHhc
Q 019740 213 TAILILYGLPRLL----------------TGSILAHEMMHAWLRLK 242 (336)
Q Consensus 213 ~~ilvl~glp~~~----------------~~~~lahe~~ha~l~~~ 242 (336)
..+-|-|-||++. ...+.+||..|+=+-.+
T Consensus 57 v~l~itytlPr~~~~~~~~~~~~~~W~~~~a~l~~HE~~H~~ia~~ 102 (161)
T PF06037_consen 57 VKLDITYTLPRWSRRAKAPPELRQRWDRFSAGLRRHEEVHGRIARE 102 (161)
T ss_pred EEEEEEEECCCccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3556778899984 67889999999987764
No 121
>cd05709 S2P-M50 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. The domain core structure appears to contain at least three transmembrane helices with a catalytic zinc atom coordinated by three conserved residues contained within the consensus sequence HExxH, together with a conserved aspartate residue. The S2P/M50 family of RIP proteases is widely distributed; in eukaryotic cells, they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum (ER) stress responses. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of sterol regulatory element-bindin
Probab=33.76 E-value=26 Score=30.73 Aligned_cols=21 Identities=33% Similarity=0.330 Sum_probs=15.6
Q ss_pred hhhhhHHHHHHHHHHHh-cCCC
Q 019740 225 LTGSILAHEMMHAWLRL-KGYP 245 (336)
Q Consensus 225 ~~~~~lahe~~ha~l~~-~g~~ 245 (336)
+.-+++.||++|++... -|.+
T Consensus 7 ~~i~i~iHE~gH~~~A~~~G~~ 28 (180)
T cd05709 7 LLISVTVHELGHALVARRLGVK 28 (180)
T ss_pred HHHHHHHHHHHHHHHHHHcCCC
Confidence 45689999999999544 4653
No 122
>PRK01345 heat shock protein HtpX; Provisional
Probab=33.57 E-value=31 Score=33.73 Aligned_cols=18 Identities=28% Similarity=0.398 Sum_probs=14.8
Q ss_pred CChhhhhhhHHHHHHHHH
Q 019740 221 LPRLLTGSILAHEMMHAW 238 (336)
Q Consensus 221 lp~~~~~~~lahe~~ha~ 238 (336)
|..--..+|||||+.|.-
T Consensus 119 L~~dEL~aVlAHElgHi~ 136 (317)
T PRK01345 119 LSPEEVAGVMAHELAHVK 136 (317)
T ss_pred CCHHHHHHHHHHHHHHHH
Confidence 566667899999999975
No 123
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=33.33 E-value=19 Score=33.14 Aligned_cols=30 Identities=20% Similarity=0.645 Sum_probs=22.8
Q ss_pred CccCCCCccCCCCCceEEcCCCceeccchhhh
Q 019740 82 PRCCSCERMEPRDTKYLSLDDGRKLCLECLDS 113 (336)
Q Consensus 82 F~C~~C~~~l~~~~~f~~~~dG~~yC~~C~~~ 113 (336)
-+|..|+..+. ..+ ....+|+++|..|+..
T Consensus 173 v~C~kCGE~~~-e~~-~~~~ng~~vC~~C~~~ 202 (206)
T COG2191 173 VRCSKCGELFM-EPR-AVVLNGKPVCKPCAEK 202 (206)
T ss_pred eeccccCcccc-cch-hhhcCCceeccccccc
Confidence 57999999885 333 3344999999999875
No 124
>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=32.88 E-value=29 Score=33.65 Aligned_cols=46 Identities=22% Similarity=0.200 Sum_probs=29.5
Q ss_pred hhhhhhhHHHHHHHHHHHhcCCC----C----------CCcc-hhhhHHHHHHHHhhhccc
Q 019740 223 RLLTGSILAHEMMHAWLRLKGYP----N----------LRPD-VEEGICQVLAHMWLESEI 268 (336)
Q Consensus 223 ~~~~~~~lahe~~ha~l~~~g~~----~----------l~~~-veeg~cq~~a~~wl~~~~ 268 (336)
.+..-.|||||+.|.-..|.|.- . +.+. .-|=-.+-+|=+|+..-.
T Consensus 167 ~~a~ayVlAHEyGHHVQ~l~Gil~~~~~~~~~~~~~~~~~~svr~ELQADC~AGvw~~~~~ 227 (292)
T PF04228_consen 167 DFAQAYVLAHEYGHHVQNLLGILDAVRQAQQGRSPAEANELSVRLELQADCFAGVWAGHAA 227 (292)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhHHHHHHHhhccCccccchHHHHHHHHHHHHHHHHhhhcc
Confidence 45566799999999999887731 1 1111 224455667888876643
No 125
>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=32.86 E-value=26 Score=31.54 Aligned_cols=14 Identities=29% Similarity=0.342 Sum_probs=11.4
Q ss_pred hhhhhHHHHHHHHH
Q 019740 225 LTGSILAHEMMHAW 238 (336)
Q Consensus 225 ~~~~~lahe~~ha~ 238 (336)
.+..++.||+|||-
T Consensus 91 ~~~~~i~HElgHaL 104 (198)
T cd04327 91 EFSRVVLHEFGHAL 104 (198)
T ss_pred hHHHHHHHHHHHHh
Confidence 44568999999996
No 126
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=32.31 E-value=21 Score=35.64 Aligned_cols=47 Identities=28% Similarity=0.322 Sum_probs=32.1
Q ss_pred EEEEecCCChhh-----hhhhHHHHHHHHHHHhcCCCCCCcchhhhHHHHHHH
Q 019740 214 AILILYGLPRLL-----TGSILAHEMMHAWLRLKGYPNLRPDVEEGICQVLAH 261 (336)
Q Consensus 214 ~ilvl~glp~~~-----~~~~lahe~~ha~l~~~g~~~l~~~veeg~cq~~a~ 261 (336)
-|+|-.||=.|+ ..++|+|||.|+--+- |...-..+-||+|.--+..
T Consensus 107 YlYitRGLlAland~sEvAAVl~HEmgHVtAnH-gi~rQ~~e~a~~ia~rvva 158 (479)
T COG4784 107 YLYITRGLLALANDSSEVAAVLAHEMGHVTANH-GIQRQQREAAEVIASRVVA 158 (479)
T ss_pred eEEEehhHHHHcCCHHHHHHHHHhhhhheecch-hHHHHHHHHHHHHHHHHHH
Confidence 467888876665 4579999999987654 5545556777777644333
No 127
>PRK01265 heat shock protein HtpX; Provisional
Probab=31.65 E-value=35 Score=33.62 Aligned_cols=24 Identities=29% Similarity=0.277 Sum_probs=17.9
Q ss_pred EEEEecC----CChhhhhhhHHHHHHHH
Q 019740 214 AILILYG----LPRLLTGSILAHEMMHA 237 (336)
Q Consensus 214 ~ilvl~g----lp~~~~~~~lahe~~ha 237 (336)
.|.|-.| |.+--..+|||||++|.
T Consensus 124 ~Ivvt~gLl~~l~~~El~aVlAHElgHi 151 (324)
T PRK01265 124 RIAITLPLLKILNRDEIKAVAGHELGHL 151 (324)
T ss_pred EEEEehHHHhhCCHHHHHHHHHHHHHHH
Confidence 3555555 56666789999999994
No 128
>PRK02391 heat shock protein HtpX; Provisional
Probab=31.65 E-value=21 Score=34.55 Aligned_cols=19 Identities=32% Similarity=0.295 Sum_probs=15.4
Q ss_pred CCChhhhhhhHHHHHHHHH
Q 019740 220 GLPRLLTGSILAHEMMHAW 238 (336)
Q Consensus 220 glp~~~~~~~lahe~~ha~ 238 (336)
.|..--..+|||||++|.-
T Consensus 127 ~L~~~El~aVlaHElgHi~ 145 (296)
T PRK02391 127 RLDPDELEAVLAHELSHVK 145 (296)
T ss_pred hCCHHHHHHHHHHHHHHHH
Confidence 4666777899999999964
No 129
>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=31.64 E-value=48 Score=32.86 Aligned_cols=38 Identities=26% Similarity=0.259 Sum_probs=21.6
Q ss_pred hhhhhhHHHHHHHHHHHh---cCCCCCCcchhhhHHHHHHH
Q 019740 224 LLTGSILAHEMMHAWLRL---KGYPNLRPDVEEGICQVLAH 261 (336)
Q Consensus 224 ~~~~~~lahe~~ha~l~~---~g~~~l~~~veeg~cq~~a~ 261 (336)
.---..|+||++||+--+ ...+.+...+.-.+.++-|-
T Consensus 220 ~~~v~tl~HE~GHa~h~~~~~~~~~~~~~~~~~~~~E~~S~ 260 (427)
T cd06459 220 LDDVFTLAHELGHAFHSYLSRDNQPYLYSDYPIFLAEIAST 260 (427)
T ss_pred hhhHHHHHHHhhHHHHHHHHccCCCcccCCCCchhhHHHHH
Confidence 344467999999987332 23332444455555555443
No 130
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=31.20 E-value=11 Score=40.76 Aligned_cols=46 Identities=20% Similarity=0.496 Sum_probs=34.1
Q ss_pred eeecCCCCCCCCCceeecCCccccccccccccC---CcCcccCCcccCCC
Q 019740 10 FRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHH---PKCDVCQNFIPTNS 56 (336)
Q Consensus 10 F~C~~C~~~L~~~~F~~~dg~~yC~~CY~~~~~---pkC~~C~~~I~~~~ 56 (336)
++|..|+....+ .-..+-+..||..|-+.++. .+|..|+.+...++
T Consensus 644 LkCs~Cn~R~Kd-~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganD 692 (698)
T KOG0978|consen 644 LKCSVCNTRWKD-AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAND 692 (698)
T ss_pred eeCCCccCchhh-HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Confidence 578889866554 23335578999999987654 47999999988775
No 131
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=31.05 E-value=25 Score=33.11 Aligned_cols=18 Identities=33% Similarity=0.281 Sum_probs=14.9
Q ss_pred CChhhhhhhHHHHHHHHH
Q 019740 221 LPRLLTGSILAHEMMHAW 238 (336)
Q Consensus 221 lp~~~~~~~lahe~~ha~ 238 (336)
|.+--.-+|||||++|.-
T Consensus 152 l~~dEl~aVlaHElgHi~ 169 (302)
T COG0501 152 LNDDELEAVLAHELGHIK 169 (302)
T ss_pred CCHHHHHHHHHHHHHHHh
Confidence 566667799999999975
No 132
>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=30.86 E-value=25 Score=32.97 Aligned_cols=12 Identities=33% Similarity=0.637 Sum_probs=10.3
Q ss_pred hhhHHHHHHHHH
Q 019740 227 GSILAHEMMHAW 238 (336)
Q Consensus 227 ~~~lahe~~ha~ 238 (336)
-.+++||||||-
T Consensus 121 ~Gti~HEl~Hal 132 (230)
T cd04282 121 KATVEHEFLHAL 132 (230)
T ss_pred CchHHHHHHHHh
Confidence 468999999996
No 133
>KOG3658 consensus Tumor necrosis factor-alpha-converting enzyme (TACE/ADAM17) and related metalloproteases [Extracellular structures]
Probab=30.79 E-value=18 Score=38.82 Aligned_cols=22 Identities=36% Similarity=0.593 Sum_probs=17.7
Q ss_pred ecC--CChhhhhhhHHHHHHHHHH
Q 019740 218 LYG--LPRLLTGSILAHEMMHAWL 239 (336)
Q Consensus 218 l~g--lp~~~~~~~lahe~~ha~l 239 (336)
-|| +|.=..--+||||+.|.|=
T Consensus 382 NYg~~Vp~kvs~lt~AHEiGHNfG 405 (764)
T KOG3658|consen 382 NYGKRVPTKVSDLTLAHEIGHNFG 405 (764)
T ss_pred ecCCccCcchhheeehhhhccccC
Confidence 377 6666777889999999993
No 134
>cd04272 ZnMc_salivary_gland_MPs Zinc-dependent metalloprotease, salivary_gland_MPs. Metalloproteases secreted by the salivary glands of arthropods.
Probab=30.59 E-value=33 Score=31.27 Aligned_cols=15 Identities=20% Similarity=0.275 Sum_probs=12.8
Q ss_pred hhhhhhHHHHHHHHH
Q 019740 224 LLTGSILAHEMMHAW 238 (336)
Q Consensus 224 ~~~~~~lahe~~ha~ 238 (336)
+....++|||++|..
T Consensus 143 ~~~~~~~AHElGH~l 157 (220)
T cd04272 143 YYGVYTMTHELAHLL 157 (220)
T ss_pred cccHHHHHHHHHHHh
Confidence 466799999999986
No 135
>PF13583 Reprolysin_4: Metallo-peptidase family M12B Reprolysin-like
Probab=30.39 E-value=26 Score=31.91 Aligned_cols=11 Identities=36% Similarity=0.534 Sum_probs=10.0
Q ss_pred hhHHHHHHHHH
Q 019740 228 SILAHEMMHAW 238 (336)
Q Consensus 228 ~~lahe~~ha~ 238 (336)
.++|||++|++
T Consensus 139 ~~~aHEiGH~l 149 (206)
T PF13583_consen 139 QTFAHEIGHNL 149 (206)
T ss_pred hHHHHHHHHHh
Confidence 66999999998
No 136
>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=30.17 E-value=45 Score=29.50 Aligned_cols=16 Identities=38% Similarity=0.451 Sum_probs=13.7
Q ss_pred hhhhhhhHHHHHHHHH
Q 019740 223 RLLTGSILAHEMMHAW 238 (336)
Q Consensus 223 ~~~~~~~lahe~~ha~ 238 (336)
.+.+..++|||++|.+
T Consensus 128 ~~~~a~~~AHElGH~l 143 (194)
T cd04269 128 LLLFAVTMAHELGHNL 143 (194)
T ss_pred hHHHHHHHHHHHHhhc
Confidence 3677899999999986
No 137
>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=29.76 E-value=41 Score=30.27 Aligned_cols=24 Identities=25% Similarity=0.146 Sum_probs=17.8
Q ss_pred hhhhhhHHHHHHHHHHHh-cCCCCC
Q 019740 224 LLTGSILAHEMMHAWLRL-KGYPNL 247 (336)
Q Consensus 224 ~~~~~~lahe~~ha~l~~-~g~~~l 247 (336)
.++.+++.||++|++... .|.+.-
T Consensus 39 ~l~~~l~iHElgH~~~A~~~G~~~~ 63 (183)
T cd06160 39 ALLAILGIHEMGHYLAARRHGVKAS 63 (183)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCcc
Confidence 356788999999999655 476533
No 138
>PF13582 Reprolysin_3: Metallo-peptidase family M12B Reprolysin-like; PDB: 3P24_C.
Probab=29.76 E-value=26 Score=28.45 Aligned_cols=12 Identities=33% Similarity=0.407 Sum_probs=10.5
Q ss_pred hhhHHHHHHHHH
Q 019740 227 GSILAHEMMHAW 238 (336)
Q Consensus 227 ~~~lahe~~ha~ 238 (336)
..++|||+.|.+
T Consensus 108 ~~~~~HEiGH~l 119 (124)
T PF13582_consen 108 VDTFAHEIGHNL 119 (124)
T ss_dssp TTHHHHHHHHHT
T ss_pred ceEeeehhhHhc
Confidence 489999999975
No 139
>COG2738 Predicted Zn-dependent protease [General function prediction only]
Probab=29.63 E-value=27 Score=32.12 Aligned_cols=28 Identities=29% Similarity=0.324 Sum_probs=22.4
Q ss_pred ecCCChhhhhhhHHHHHHHHHHHhcCCC
Q 019740 218 LYGLPRLLTGSILAHEMMHAWLRLKGYP 245 (336)
Q Consensus 218 l~glp~~~~~~~lahe~~ha~l~~~g~~ 245 (336)
-|+=|-+..-++.|||..||..-..+|+
T Consensus 84 ~y~g~Sia~~aVAAHEVGHAiQd~~~Y~ 111 (226)
T COG2738 84 NYYGPSIAAIAVAAHEVGHAIQDQEDYA 111 (226)
T ss_pred ccCCccHHHHHHHHHHhhHHHhhhcccH
Confidence 4666788888999999999987666654
No 140
>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=29.56 E-value=28 Score=31.37 Aligned_cols=12 Identities=42% Similarity=0.800 Sum_probs=10.3
Q ss_pred hhhHHHHHHHHH
Q 019740 227 GSILAHEMMHAW 238 (336)
Q Consensus 227 ~~~lahe~~ha~ 238 (336)
-.+++||+|||-
T Consensus 78 ~G~i~HEl~HaL 89 (182)
T cd04283 78 KGIIQHELLHAL 89 (182)
T ss_pred cchHHHHHHHHh
Confidence 468999999995
No 141
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=29.37 E-value=29 Score=25.05 Aligned_cols=28 Identities=21% Similarity=0.490 Sum_probs=16.3
Q ss_pred eecCCCCCCCCCceeecCCccccc-cccc
Q 019740 11 RCHSCNLPITDVEFSMSGNRPYHK-HCYK 38 (336)
Q Consensus 11 ~C~~C~~~L~~~~F~~~dg~~yC~-~CY~ 38 (336)
-|..|...+....-+.+||+.||. .|-.
T Consensus 9 aC~~C~C~V~~~~Ai~~dGk~YCS~aCA~ 37 (52)
T PF02069_consen 9 ACPSCSCVVSEEEAIQKDGKYYCSEACAN 37 (52)
T ss_dssp SSTT----B-TTTSEESSS-EESSHHHHH
T ss_pred cCCCCEeEECchHhHHhCCEeeecHHHhc
Confidence 367888888866778899999995 4543
No 142
>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=28.80 E-value=26 Score=36.96 Aligned_cols=13 Identities=38% Similarity=0.946 Sum_probs=11.7
Q ss_pred hhhHHHHHHHHHH
Q 019740 227 GSILAHEMMHAWL 239 (336)
Q Consensus 227 ~~~lahe~~ha~l 239 (336)
+.++|||++|.|-
T Consensus 289 ~~vIaHEIAHSWt 301 (613)
T KOG1047|consen 289 VDVIAHEIAHSWT 301 (613)
T ss_pred hhHHHHHhhhhhc
Confidence 5899999999994
No 143
>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=28.44 E-value=48 Score=36.94 Aligned_cols=41 Identities=20% Similarity=0.421 Sum_probs=26.7
Q ss_pred hhhhHHHHHHHHHHHhc-CCCC-CCcchhhhHHHHHHHHhhhc
Q 019740 226 TGSILAHEMMHAWLRLK-GYPN-LRPDVEEGICQVLAHMWLES 266 (336)
Q Consensus 226 ~~~~lahe~~ha~l~~~-g~~~-l~~~veeg~cq~~a~~wl~~ 266 (336)
..+++|||+.|-|.-=. -.+. -...+-||+.-.+..+|.+.
T Consensus 283 i~~VIaHElaHqWfGNlVT~~~W~~LWLnEGfAty~e~~~~~~ 325 (863)
T TIGR02414 283 IESVIAHEYFHNWTGNRVTCRDWFQLSLKEGLTVFRDQEFSAD 325 (863)
T ss_pred HHHHHHHHHHHHHhcceeeecchhhhhhhhhHHHHHHHHHHHH
Confidence 35899999999995210 0111 12457999998888766543
No 144
>PRK09672 phage exclusion protein Lit; Provisional
Probab=28.21 E-value=69 Score=31.31 Aligned_cols=48 Identities=25% Similarity=0.202 Sum_probs=37.0
Q ss_pred CCChhhhhhhHHHHHHHHHHHhcCCCCCC-cchhhhHHHHHHHHhhhcc
Q 019740 220 GLPRLLTGSILAHEMMHAWLRLKGYPNLR-PDVEEGICQVLAHMWLESE 267 (336)
Q Consensus 220 glp~~~~~~~lahe~~ha~l~~~g~~~l~-~~veeg~cq~~a~~wl~~~ 267 (336)
.|=-..++-|+.||+.|+.+-..++.... -.-||==|-..|--||-..
T Consensus 159 dLfl~A~a~i~~HEiaHv~~~h~~~~~~e~s~~eE~eaDs~At~~il~~ 207 (305)
T PRK09672 159 DLFLCALAWILLHEIAHVEFQHSSLESNEDSIQEEKEADSYATNWLLSK 207 (305)
T ss_pred HHHHHHHHHHHHHHHHHHHhccccccCchHHHHHHHHHHHHHHHHHHhc
Confidence 34456788999999999999998864444 3456777999999997653
No 145
>COG0308 PepN Aminopeptidase N [Amino acid transport and metabolism]
Probab=28.09 E-value=31 Score=38.34 Aligned_cols=38 Identities=26% Similarity=0.504 Sum_probs=28.6
Q ss_pred hHHHHHHHHHHH----hcCCCCCCcchhhhHHHHHHHHhhhccc
Q 019740 229 ILAHEMMHAWLR----LKGYPNLRPDVEEGICQVLAHMWLESEI 268 (336)
Q Consensus 229 ~lahe~~ha~l~----~~g~~~l~~~veeg~cq~~a~~wl~~~~ 268 (336)
++||||.|.|.- ++-. -...+-||+--++.+.|.+...
T Consensus 310 viaHElaHqWfGnlVT~~~W--~~lWLnEgfat~~e~~~~~~~~ 351 (859)
T COG0308 310 VIAHELAHQWFGNLVTMKWW--DDLWLNEGFATFREVLWSEDLG 351 (859)
T ss_pred HHHHHHhhhcccceeeccCH--HHHHHhhhhHHHHHHHHHHHhc
Confidence 999999999941 1111 2367889999999999987764
No 146
>KOG3314 consensus Ku70-binding protein [Replication, recombination and repair]
Probab=28.05 E-value=34 Score=30.64 Aligned_cols=16 Identities=25% Similarity=0.538 Sum_probs=12.8
Q ss_pred hhhhHHHHHHHHHHHh
Q 019740 226 TGSILAHEMMHAWLRL 241 (336)
Q Consensus 226 ~~~~lahe~~ha~l~~ 241 (336)
..-+++|||.|||=-+
T Consensus 91 ~n~vv~HElIH~fDd~ 106 (194)
T KOG3314|consen 91 VNQVVIHELIHAFDDC 106 (194)
T ss_pred HHHHHHHHHHHHHHhh
Confidence 4568999999999554
No 147
>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=27.45 E-value=34 Score=23.46 Aligned_cols=14 Identities=36% Similarity=0.930 Sum_probs=10.9
Q ss_pred eeecCCCCCCCCCc
Q 019740 10 FRCHSCNLPITDVE 23 (336)
Q Consensus 10 F~C~~C~~~L~~~~ 23 (336)
|+|..|+++|.+..
T Consensus 1 ~~C~~C~~~i~g~r 14 (46)
T cd02249 1 YSCDGCLKPIVGVR 14 (46)
T ss_pred CCCcCCCCCCcCCE
Confidence 57899999887743
No 148
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=27.42 E-value=21 Score=29.16 Aligned_cols=31 Identities=23% Similarity=0.574 Sum_probs=20.1
Q ss_pred CCCCccCCCCccCCCCCceEEcCCCceeccch
Q 019740 79 DGTPRCCSCERMEPRDTKYLSLDDGRKLCLEC 110 (336)
Q Consensus 79 ~~CF~C~~C~~~l~~~~~f~~~~dG~~yC~~C 110 (336)
..=|.|.+|-..-- ..+-....+|.++|..|
T Consensus 68 ~DEFTCssCFLV~H-RSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 68 ADEFTCSSCFLVHH-RSQLAREKDGQPICRDC 98 (99)
T ss_pred CCceeeeeeeeEec-hhhhccccCCCEecccc
Confidence 34499999975432 22222344899999998
No 149
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=27.36 E-value=38 Score=32.60 Aligned_cols=16 Identities=13% Similarity=0.513 Sum_probs=12.8
Q ss_pred CCCeeecCCCCCCCCC
Q 019740 7 PECFRCHSCNLPITDV 22 (336)
Q Consensus 7 ~~CF~C~~C~~~L~~~ 22 (336)
...++|..|++..+..
T Consensus 128 ~~r~~c~eCgk~ysT~ 143 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTS 143 (279)
T ss_pred CCceeccccccccccc
Confidence 3478999999998763
No 150
>cd06461 M2_ACE Peptidase family M2 Angiotensin converting enzyme (ACE, EC 3.4.15.1) is a membrane-bound, zinc dependent dipeptidase that catalyzes the conversion of the decapeptide angiotensin I to the potent vasopressor ocatapeptide angiotensin II, by removing two C-terminal amino acids. There are two forms of the enzyme in humans, the ubiquitous somatic ACE and the sperm-specific germinal ACE, both encoded by the same gene through transcription from alternative promoters. Somatic ACE has two tandem active sites with distinct catalytic properties, whereas germinal ACE, the function of which is largely unknown, has just a single active site. Recently, an ACE homolog, ACE2, has been identified in humans that differs from ACE; it preferentially removes carboxy-terminal hydrophobic or basic amino acids and appears to be important in cardiac function. ACE homologs (also known as members of the M2 gluzincin family) have been found in a wide variety of species, including those that neither h
Probab=27.12 E-value=58 Score=33.81 Aligned_cols=34 Identities=26% Similarity=0.370 Sum_probs=23.4
Q ss_pred hHHHHHHHHHHHhcCCCCCC--------cchhhhHHHHHHHHh
Q 019740 229 ILAHEMMHAWLRLKGYPNLR--------PDVEEGICQVLAHMW 263 (336)
Q Consensus 229 ~lahe~~ha~l~~~g~~~l~--------~~veeg~cq~~a~~w 263 (336)
++-|||+||+.-+. |++++ |...|-+|+++|..-
T Consensus 250 t~~HE~GH~~yy~~-y~~~p~~~r~~anp~fheav~e~~smS~ 291 (477)
T cd06461 250 TVHHEMGHIQYYLQ-YKDQPVLFREGANPGFHEAVGDAIALSV 291 (477)
T ss_pred HHHHHHHHHHHHHH-hccCCHHHhCCCCCChHHHHHHHHHHhc
Confidence 46699999986544 44443 555668899987654
No 151
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=26.41 E-value=39 Score=20.46 Aligned_cols=21 Identities=24% Similarity=0.504 Sum_probs=11.2
Q ss_pred ccCCCCccCCCCCceEEcCCCceeccchhh
Q 019740 83 RCCSCERMEPRDTKYLSLDDGRKLCLECLD 112 (336)
Q Consensus 83 ~C~~C~~~l~~~~~f~~~~dG~~yC~~C~~ 112 (336)
.|..|+..++ ++..||..|-.
T Consensus 4 ~Cp~Cg~~~~---------~~~~fC~~CG~ 24 (26)
T PF13248_consen 4 FCPNCGAEID---------PDAKFCPNCGA 24 (26)
T ss_pred CCcccCCcCC---------cccccChhhCC
Confidence 3666666543 34455666643
No 152
>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=26.31 E-value=32 Score=36.15 Aligned_cols=16 Identities=38% Similarity=0.355 Sum_probs=12.9
Q ss_pred hhhhhhhHHHHHHHHH
Q 019740 223 RLLTGSILAHEMMHAW 238 (336)
Q Consensus 223 ~~~~~~~lahe~~ha~ 238 (336)
.+---.+||||++||+
T Consensus 375 ~~~dv~TLaHElGHa~ 390 (591)
T TIGR00181 375 TLNSVFTLAHELGHSM 390 (591)
T ss_pred CcchHHHHHHHhhhHH
Confidence 3455689999999998
No 153
>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=26.10 E-value=58 Score=21.21 Aligned_cols=36 Identities=19% Similarity=0.499 Sum_probs=22.1
Q ss_pred cCCCCccCCCCCceEEcCCCceeccchhhhcccCCCCC
Q 019740 84 CCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHEC 121 (336)
Q Consensus 84 C~~C~~~l~~~~~f~~~~dG~~yC~~C~~~~v~~~~~C 121 (336)
|..|...+. ...+...=|..||.+|..+.+.....|
T Consensus 1 C~iC~~~~~--~~~~~~~CGH~fC~~C~~~~~~~~~~C 36 (39)
T PF13923_consen 1 CPICLDELR--DPVVVTPCGHSFCKECIEKYLEKNPKC 36 (39)
T ss_dssp ETTTTSB-S--SEEEECTTSEEEEHHHHHHHHHCTSB-
T ss_pred CCCCCCccc--CcCEECCCCCchhHHHHHHHHHCcCCC
Confidence 456666553 354456679999999988764443333
No 154
>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=25.42 E-value=41 Score=22.90 Aligned_cols=30 Identities=20% Similarity=0.702 Sum_probs=18.2
Q ss_pred eeecCCCCCCCCCceee--cCCcccccccccc
Q 019740 10 FRCHSCNLPITDVEFSM--SGNRPYHKHCYKE 39 (336)
Q Consensus 10 F~C~~C~~~L~~~~F~~--~dg~~yC~~CY~~ 39 (336)
+.|..|+++|.+..|.- =.+--+|.+||.+
T Consensus 5 ~~C~~C~~~i~g~ry~C~~C~d~dlC~~Cf~~ 36 (44)
T smart00291 5 YSCDTCGKPIVGVRYHCLVCPDYDLCQSCFAK 36 (44)
T ss_pred cCCCCCCCCCcCCEEECCCCCCccchHHHHhC
Confidence 45788888887765531 1234556666653
No 155
>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=25.05 E-value=34 Score=29.35 Aligned_cols=16 Identities=38% Similarity=0.191 Sum_probs=13.2
Q ss_pred ChhhhhhhHHHHHHHH
Q 019740 222 PRLLTGSILAHEMMHA 237 (336)
Q Consensus 222 p~~~~~~~lahe~~ha 237 (336)
+..-.-.|+.||+.||
T Consensus 103 ~~~~~~~~~~HEiGHa 118 (157)
T cd04278 103 GGTDLFSVAAHEIGHA 118 (157)
T ss_pred ccchHHHHHHHHhccc
Confidence 3455778999999999
No 156
>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=25.01 E-value=39 Score=29.49 Aligned_cols=19 Identities=42% Similarity=0.742 Sum_probs=13.9
Q ss_pred ChhhhhhhHHHHHHHHHHHh
Q 019740 222 PRLLTGSILAHEMMHAWLRL 241 (336)
Q Consensus 222 p~~~~~~~lahe~~ha~l~~ 241 (336)
+....|.+|+||++| ||-|
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 366779999999999 5555
No 157
>PRK11595 DNA utilization protein GntX; Provisional
Probab=24.80 E-value=46 Score=30.66 Aligned_cols=37 Identities=16% Similarity=0.385 Sum_probs=23.0
Q ss_pred eecCCCCCCCCCceeecCCcccccccccccc--CCcCcccCCccc
Q 019740 11 RCHSCNLPITDVEFSMSGNRPYHKHCYKEQH--HPKCDVCQNFIP 53 (336)
Q Consensus 11 ~C~~C~~~L~~~~F~~~dg~~yC~~CY~~~~--~pkC~~C~~~I~ 53 (336)
+|..|++++... ....|..|...+. .+.|..|+.++.
T Consensus 7 ~C~~C~~~~~~~------~~~lC~~C~~~l~~~~~~C~~Cg~~~~ 45 (227)
T PRK11595 7 LCWLCRMPLALS------HWGICSVCSRALRTLKTCCPQCGLPAT 45 (227)
T ss_pred cCccCCCccCCC------CCcccHHHHhhCCcccCcCccCCCcCC
Confidence 366777777432 1247888876542 356888887643
No 158
>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=24.73 E-value=36 Score=30.21 Aligned_cols=12 Identities=42% Similarity=0.631 Sum_probs=10.1
Q ss_pred hhhHHHHHHHHH
Q 019740 227 GSILAHEMMHAW 238 (336)
Q Consensus 227 ~~~lahe~~ha~ 238 (336)
-.++.||+|||-
T Consensus 75 ~g~v~HE~~Hal 86 (180)
T cd04280 75 LGTIVHELMHAL 86 (180)
T ss_pred CchhHHHHHHHh
Confidence 368899999994
No 159
>PF07607 DUF1570: Protein of unknown function (DUF1570); InterPro: IPR011464 This entry represents hypothetical proteins confined to bacteria.
Probab=24.32 E-value=85 Score=26.72 Aligned_cols=32 Identities=28% Similarity=0.402 Sum_probs=23.9
Q ss_pred hhHHHHHHHHHHHhcCC-C---CCCcchhhhHHHHH
Q 019740 228 SILAHEMMHAWLRLKGY-P---NLRPDVEEGICQVL 259 (336)
Q Consensus 228 ~~lahe~~ha~l~~~g~-~---~l~~~veeg~cq~~ 259 (336)
+.++||..|-=+.--|. + .-|..|-|||...+
T Consensus 3 ~T~~HEa~HQl~~N~Gl~~r~~~~P~Wv~EGlA~yF 38 (128)
T PF07607_consen 3 ATIAHEATHQLAFNTGLHPRLADWPRWVSEGLATYF 38 (128)
T ss_pred hHHHHHHHHHHHHHccccccCCCCchHHHHhHHHHc
Confidence 67999999988777673 3 44567888887655
No 160
>PF11928 DUF3446: Domain of unknown function (DUF3446); InterPro: IPR021849 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 80 to 99 amino acids in length. This domain is found associated with PF00096 from PFAM. This domain has a single completely conserved residue P that may be functionally important.
Probab=24.12 E-value=85 Score=24.92 Aligned_cols=9 Identities=22% Similarity=0.346 Sum_probs=6.5
Q ss_pred hhhHHHHHH
Q 019740 252 EEGICQVLA 260 (336)
Q Consensus 252 eeg~cq~~a 260 (336)
-|||=+++.
T Consensus 17 ~E~iislvS 25 (84)
T PF11928_consen 17 PEPIISLVS 25 (84)
T ss_pred cchhHHHhh
Confidence 677777776
No 161
>PHA02624 large T antigen; Provisional
Probab=23.85 E-value=1.6e+02 Score=31.87 Aligned_cols=23 Identities=30% Similarity=0.375 Sum_probs=19.7
Q ss_pred CCchHHHHHHHHHhhhhhcCCCC
Q 019740 302 KRSDFEKDLGKFFKHQIESDTSS 324 (336)
Q Consensus 302 ~~~~~~~~l~~~~~~~i~~d~s~ 324 (336)
++.+|-.-|.+|+.+.|-++..+
T Consensus 149 ~p~dfp~~L~~flS~Ai~sNkt~ 171 (647)
T PHA02624 149 APNDFPSCLLAFLSHAIFSNKTL 171 (647)
T ss_pred ChhhhHHHHHHHHHHHHhhcCCC
Confidence 67799999999999999877653
No 162
>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=23.42 E-value=54 Score=25.89 Aligned_cols=10 Identities=40% Similarity=0.810 Sum_probs=5.8
Q ss_pred cCcccCCccc
Q 019740 44 KCDVCQNFIP 53 (336)
Q Consensus 44 kC~~C~~~I~ 53 (336)
.|..|+.+|+
T Consensus 2 ~C~HCg~~~p 11 (88)
T PF12156_consen 2 KCYHCGLPVP 11 (88)
T ss_pred CCCCCCCCCC
Confidence 3556666664
No 163
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=23.40 E-value=61 Score=24.12 Aligned_cols=40 Identities=18% Similarity=0.420 Sum_probs=25.3
Q ss_pred CccCCCCccCCCCCceEEcCCCceeccchhhhcccCCCCCCchhhHHHHHHhhccceeccccccchhc
Q 019740 82 PRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVE 149 (336)
Q Consensus 82 F~C~~C~~~l~~~~~f~~~~dG~~yC~~C~~~~v~~~~~C~~c~~~I~~f~~glg~~i~~~~p~~lV~ 149 (336)
..|-.|+-+|. +..+.+.++|..|... -||.+.+|++|.+
T Consensus 9 LaCP~~kg~L~-----~~~~~~~L~c~~~~~a-----------------------YpI~dGIPvlL~~ 48 (60)
T COG2835 9 LACPVCKGPLV-----YDEEKQELICPRCKLA-----------------------YPIRDGIPVLLPD 48 (60)
T ss_pred eeccCcCCcce-----EeccCCEEEecccCce-----------------------eecccCccccCch
Confidence 34666665553 2333556777777443 5788999998864
No 164
>PRK12495 hypothetical protein; Provisional
Probab=23.31 E-value=39 Score=31.53 Aligned_cols=25 Identities=20% Similarity=0.509 Sum_probs=16.0
Q ss_pred CCeeecCCCCCCCCCceeecCCcccccccc
Q 019740 8 ECFRCHSCNLPITDVEFSMSGNRPYHKHCY 37 (336)
Q Consensus 8 ~CF~C~~C~~~L~~~~F~~~dg~~yC~~CY 37 (336)
--|.|..|+.||. ...|..+|..|-
T Consensus 41 sa~hC~~CG~PIp-----a~pG~~~Cp~CQ 65 (226)
T PRK12495 41 TNAHCDECGDPIF-----RHDGQEFCPTCQ 65 (226)
T ss_pred chhhcccccCccc-----CCCCeeECCCCC
Confidence 3467888888885 236666555554
No 165
>cd06163 S2P-M50_PDZ_RseP-like RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. In Escherichia coli, the S2P homolog RseP is involved in the sigmaE pathway of extracytoplasmic stress responses. Also included in this group are such homologs as Bacillus subtilis YluC, Mycobacterium tuberculosis Rv2869c S2P, and Bordetella bronchiseptica HurP. Rv2869c S2P appears to have a role in the regulation of prokaryotic lipid biosynthesis and membrane composition and YluC of Bacillus has a role in transducing membrane stress. This group includes bacterial and eukaryotic S2P/M50s homologs with either one or two PDZ domains present. PDZ domains are believed to have a regulatory role. The RseP PDZ domain is required for the inhibitory reaction that prevents cleavage of its substrate, RseA.
Probab=22.84 E-value=54 Score=29.47 Aligned_cols=21 Identities=29% Similarity=0.240 Sum_probs=15.9
Q ss_pred hhhhhHHHHHHHHHHHh-cCCC
Q 019740 225 LTGSILAHEMMHAWLRL-KGYP 245 (336)
Q Consensus 225 ~~~~~lahe~~ha~l~~-~g~~ 245 (336)
+..+++-||+.|.|... .|.+
T Consensus 8 l~~~v~iHElGH~~~Ar~~Gv~ 29 (182)
T cd06163 8 LGILIFVHELGHFLVAKLFGVK 29 (182)
T ss_pred HHHHHHHHHHHHHHHHHHcCCe
Confidence 56689999999999654 3653
No 166
>KOG2661 consensus Peptidase family M48 [Posttranslational modification, protein turnover, chaperones]
Probab=22.56 E-value=55 Score=32.64 Aligned_cols=27 Identities=30% Similarity=0.482 Sum_probs=18.5
Q ss_pred EEEecC-CChh----hhhhhHHHHHHHHHHHh
Q 019740 215 ILILYG-LPRL----LTGSILAHEMMHAWLRL 241 (336)
Q Consensus 215 ilvl~g-lp~~----~~~~~lahe~~ha~l~~ 241 (336)
|.|..| ||.. -...+||||++||-.|-
T Consensus 259 vfVFtgiLn~ck~ddglAtvLgHE~aHaVarH 290 (424)
T KOG2661|consen 259 VFVFTGILNSCKDDDGLATVLGHEIAHAVARH 290 (424)
T ss_pred EEEEechhhcccChHHHHHHHHHHHHHHHHHH
Confidence 345555 4432 24579999999998885
No 167
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=22.41 E-value=54 Score=24.19 Aligned_cols=30 Identities=17% Similarity=0.485 Sum_probs=20.5
Q ss_pred cCCCCccCCCCCceEEcCCCceec-cchhhh
Q 019740 84 CCSCERMEPRDTKYLSLDDGRKLC-LECLDS 113 (336)
Q Consensus 84 C~~C~~~l~~~~~f~~~~dG~~yC-~~C~~~ 113 (336)
|.-|++.|..+...++..+.+.+| .+|-..
T Consensus 19 C~~C~k~L~~~~DiymYrGd~aFCS~ECR~~ 49 (58)
T PF04570_consen 19 CYLCKKKLDPGKDIYMYRGDKAFCSEECRSQ 49 (58)
T ss_pred HHccCCCCCCCCCeeeeccccccccHHHHHH
Confidence 777888887666666666777888 346544
No 168
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=22.22 E-value=43 Score=21.83 Aligned_cols=11 Identities=27% Similarity=1.005 Sum_probs=8.5
Q ss_pred eeecCCCCCCC
Q 019740 10 FRCHSCNLPIT 20 (336)
Q Consensus 10 F~C~~C~~~L~ 20 (336)
|+|..|+..+.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 68888888664
No 169
>COG3590 PepO Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]
Probab=21.81 E-value=23 Score=37.46 Aligned_cols=16 Identities=25% Similarity=0.549 Sum_probs=13.3
Q ss_pred hhhhHHHHHHHHHHHh
Q 019740 226 TGSILAHEMMHAWLRL 241 (336)
Q Consensus 226 ~~~~lahe~~ha~l~~ 241 (336)
-|+|.+|||.|+|=-.
T Consensus 487 IGaVIgHEI~HgFDdq 502 (654)
T COG3590 487 IGAVIGHEIGHGFDDQ 502 (654)
T ss_pred ccceehhhhcccccCC
Confidence 4899999999999544
No 170
>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=21.28 E-value=47 Score=31.75 Aligned_cols=18 Identities=22% Similarity=0.305 Sum_probs=14.3
Q ss_pred hhhhhHHHHHHHHHHHhc
Q 019740 225 LTGSILAHEMMHAWLRLK 242 (336)
Q Consensus 225 ~~~~~lahe~~ha~l~~~ 242 (336)
.+..|+.||++|.+..|.
T Consensus 215 ~~~~v~vHE~GHsf~~La 232 (264)
T PF09471_consen 215 SFKQVVVHEFGHSFGGLA 232 (264)
T ss_dssp THHHHHHHHHHHHTT---
T ss_pred cccceeeeeccccccccc
Confidence 788999999999999995
No 171
>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=21.21 E-value=50 Score=32.30 Aligned_cols=34 Identities=24% Similarity=0.370 Sum_probs=24.7
Q ss_pred CCChhhhhhhHHHHHHHHHHHhcCCCCCCcchhhhHHHHHHHHh
Q 019740 220 GLPRLLTGSILAHEMMHAWLRLKGYPNLRPDVEEGICQVLAHMW 263 (336)
Q Consensus 220 glp~~~~~~~lahe~~ha~l~~~g~~~l~~~veeg~cq~~a~~w 263 (336)
.+|.+..-.++||||+|- .|| .-|.=|+.+|++-
T Consensus 190 ~~p~~~~P~T~~HElAHq----~G~------a~E~EANFiayLa 223 (318)
T PF12725_consen 190 DLPPYSLPFTICHELAHQ----LGF------ASEDEANFIAYLA 223 (318)
T ss_pred CCCcccccHHHHHHHHHH----hCC------CCHHHHHHHHHHH
Confidence 488899999999999993 354 2355566666665
No 172
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=21.17 E-value=47 Score=22.46 Aligned_cols=12 Identities=25% Similarity=0.816 Sum_probs=9.3
Q ss_pred eeecCCCCCCCC
Q 019740 10 FRCHSCNLPITD 21 (336)
Q Consensus 10 F~C~~C~~~L~~ 21 (336)
|+|..|+..+..
T Consensus 6 y~C~~Cg~~fe~ 17 (42)
T PF09723_consen 6 YRCEECGHEFEV 17 (42)
T ss_pred EEeCCCCCEEEE
Confidence 789999877754
No 173
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=21.14 E-value=50 Score=35.47 Aligned_cols=17 Identities=12% Similarity=-0.116 Sum_probs=12.9
Q ss_pred hhhhhcCCCCCCchhhh
Q 019740 315 KHQIESDTSSAYGDGLG 331 (336)
Q Consensus 315 ~~~i~~d~s~~yg~gfr 331 (336)
+..+..|.|..|=++.+
T Consensus 483 ~~~s~~~~s~~~v~~~~ 499 (694)
T KOG4443|consen 483 KPNSAVQISEPGVGSEA 499 (694)
T ss_pred cCCcccccccccccccc
Confidence 46778888888877765
No 174
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.05 E-value=84 Score=29.51 Aligned_cols=54 Identities=13% Similarity=0.362 Sum_probs=36.5
Q ss_pred CCeeecCCCCCCCCCceeecCCcccccccccc-----ccCCcCcccCCcccCCCCceEEEee
Q 019740 8 ECFRCHSCNLPITDVEFSMSGNRPYHKHCYKE-----QHHPKCDVCQNFIPTNSAGLIEYRA 64 (336)
Q Consensus 8 ~CF~C~~C~~~L~~~~F~~~dg~~yC~~CY~~-----~~~pkC~~C~~~I~~~~~g~i~~~~ 64 (336)
.+|-|..|=. ++...-..-=|.+||=.|..+ .....|.+|+-.|..+. +|-..+
T Consensus 46 ~~FdCNICLd-~akdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~--vvPlYG 104 (230)
T KOG0823|consen 46 GFFDCNICLD-LAKDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDT--VVPLYG 104 (230)
T ss_pred Cceeeeeecc-ccCCCEEeecccceehHHHHHHHhhcCCCeeCCccccccccce--EEeeec
Confidence 4788888833 333345556789999999865 34456899999888753 554444
No 175
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=20.59 E-value=65 Score=19.92 Aligned_cols=12 Identities=42% Similarity=0.908 Sum_probs=6.8
Q ss_pred CcCcccCCcccC
Q 019740 43 PKCDVCQNFIPT 54 (336)
Q Consensus 43 pkC~~C~~~I~~ 54 (336)
.+|..|...|..
T Consensus 2 ~~C~rC~~~~~~ 13 (30)
T PF06827_consen 2 EKCPRCWNYIED 13 (30)
T ss_dssp SB-TTT--BBEE
T ss_pred CcCccCCCcceE
Confidence 478888888875
No 176
>cd06258 Peptidase_M3_like The peptidase M3-like family, also called neurolysin-like family, is part of the "zincins" metallopeptidases, and includes M3, M2 and M32 families of metallopeptidases. The M3 family is subdivided into two subfamilies: the widespread M3A, which comprises a number of high-molecular mass endo- and exopeptidases from bacteria, archaea, protozoa, fungi, plants and animals, and the small M3B, whose members are enzymes primarily from bacteria. Well-known mammalian/eukaryotic M3A endopeptidases are the thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (alias endopeptidase 3.4.24.16), and the mitochondrial intermediate peptidase. The first two are intracellular oligopeptidases, which act only on relatively short substrates of less than 20 amino acid residues, while the latter cleaves N-terminal octapeptides from proteins during their import into the mitochondria. The M3A subfamily also contains several bacterial endopeptidases, collectively called olig
Probab=20.31 E-value=1.5e+02 Score=28.96 Aligned_cols=32 Identities=28% Similarity=0.318 Sum_probs=18.7
Q ss_pred hhHHHHHHHHHHHh--c-CCCC-CCcchhhhHHHHH
Q 019740 228 SILAHEMMHAWLRL--K-GYPN-LRPDVEEGICQVL 259 (336)
Q Consensus 228 ~~lahe~~ha~l~~--~-g~~~-l~~~veeg~cq~~ 259 (336)
..|+||++||.--+ + .++. +...++-++.++.
T Consensus 156 ~tl~HE~GHa~h~~l~~~~~~~~~g~~~~~~~~E~~ 191 (365)
T cd06258 156 NTLFHEFGHAVHFLLIQQRYPFQERTPTSTDFAEAQ 191 (365)
T ss_pred HHHHHHHhHHHHHHHhcCCCCcCCCCCCCccHHhcc
Confidence 56999999999443 2 3443 3244555555543
No 177
>PF01432 Peptidase_M3: Peptidase family M3 This Prosite motif covers only the active site. This family belongs to family M3 of the peptidase classification.; InterPro: IPR001567 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M3 (clan MA(E)), subfamilies M3A and M3B. The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. The Thimet oligopeptidase family, is a large family of archaeal, bacterial and eukaryotic oligopeptidases that cleave medium sized peptides. The group contains: mitochondrial intermediate peptidase (3.4.24.59 from EC) Neurolysin, mitochondrial precursor, (3.4.24.16 from EC) Thimet oligopeptidase (3.4.24.15 from EC) Dipeptidyl carboxypeptidase (3.4.15.5 from EC) Oligopeptidase A (3.4.24.70 from EC) Oligoendopeptidase F ; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2QR4_B 3CE2_A 1Y79_1 2H1J_A 2H1N_A 2O36_A 1S4B_P 2O3E_A 1I1I_P.
Probab=20.21 E-value=1.6e+02 Score=29.75 Aligned_cols=16 Identities=38% Similarity=0.314 Sum_probs=13.2
Q ss_pred hhhhHHHHHHHHHHHh
Q 019740 226 TGSILAHEMMHAWLRL 241 (336)
Q Consensus 226 ~~~~lahe~~ha~l~~ 241 (336)
--..|+||++||+--+
T Consensus 242 ~v~tLfHE~GHa~H~~ 257 (458)
T PF01432_consen 242 DVETLFHEFGHAMHSL 257 (458)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHhHHHHHH
Confidence 4678999999999555
No 178
>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=20.08 E-value=86 Score=21.79 Aligned_cols=30 Identities=23% Similarity=0.610 Sum_probs=17.9
Q ss_pred ccCCCCccCCCCCceEEcCC-Cceeccchhhh
Q 019740 83 RCCSCERMEPRDTKYLSLDD-GRKLCLECLDS 113 (336)
Q Consensus 83 ~C~~C~~~l~~~~~f~~~~d-G~~yC~~C~~~ 113 (336)
.|..|+..++ ..+|..+.. +.-+|..||..
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 4777777775 445543322 34678888765
Done!